Phyre 2 Results for P24203

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P24203
Date | Thu Jan 5 11:41:12 GMT 2012
Unique Job ID | fdfbaccd160fb744

Summary |

Top model
Image coloured by rainbow N → C terminus
| Close Jmol

Model (left) based on template c1nijA_
Top template information
PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein yjia; PDBTitle: yjia protein
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
317 residues (100% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | N | P | I | A | V | T | L | L | T | G | F | L | G | A | G | K | T | T | L | L | R | H | I | L | N | E | Q | H | G | Y | K | I | A | V | I | E | N | E | F | G | E | V | S | V | D | D | Q | L | I | G | D | R | A | T | Q | I | K | T | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | T | N | G | C | I | C | C | S | R | S | N | E | L | E | D | A | L | L | D | L | L | D | N | L | D | K | G | N | I | Q | F | D | R | L | V | I | E | C | T | G | M | A | D | P | G | P | I | I | Q | T | F | F | S | H | E | V | L | C | Q | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | Y | L | L | D | G | V | I | A | L | V | D | A | V | H | A | D | E | Q | M | N | Q | F | T | I | A | Q | S | Q | V | G | Y | A | D | R | I | L | L | T | K | T | D | V | A | G | E | A | E | K | L | H | E | R | L | A | R | I | N | A | R | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | P | V | Y | T | V | T | H | G | D | I | D | L | G | L | L | F | N | T | N | G | F | M | L | E | E | N | V | V | S | T | K | P | R | F | H | F | I | A | D | K | Q | N | D | I | S | S | I | V | V | E | L | D | Y | P | V | D | I | S | E | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  | ? | ? | ? | ? |  | ? |  | ? | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | S | R | V | M | E | N | L | L | L | E | S | A | D | K | L | L | R | Y | K | G | M | L | W | I | D | G | E | P | N | R | L | L | F | Q | G | V | Q | R | L | Y | S | A | D | W | D | R | P | W | G | D | E | K | P | H | S | T | M | V | F | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | .
Sequence |  | G | I | Q | L | P | E | E | E | I | R | A | A | F | A | G | L | R | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |

Confidence Key
High(9) |  |  |  |  |  |  |  |  |  |  | Low (0)

? | Disordered
| Alpha helix
| Beta strand

Domain analysis |

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank | Aligned region
--- | ---
1 |
| c1nijA_ |

### PDB 1nij chain A

Region: 2 - 318
Aligned: 317
Modelled: 317
Confidence: 100.0%
Identity: 100%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yjia;
PDBTitle: yjia protein

Phyre2
2 |
| d1nija1 |

### PDB 1nij chain A domain 1

Region: 2 - 223
Aligned: 222
Modelled: 222
Confidence: 100.0%
Identity: 100%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Nitrogenase iron protein-like

Phyre2
3 |
| d1nija2 |

### PDB 1nij chain A domain 2

Region: 224 - 318
Aligned: 95
Modelled: 95
Confidence: 99.9%
Identity: 100%
Fold: Hypothetical protein YjiA, C-terminal domain
Superfamily: Hypothetical protein YjiA, C-terminal domain
Family: Hypothetical protein YjiA, C-terminal domain

Phyre2
4 |
| c2hf9A_ |

### PDB 2hf9 chain A

Region: 2 - 186
Aligned: 164
Modelled: 185
Confidence: 99.5%
Identity: 25%
PDB header:hydrolase, metal binding protein
Chain: A: PDB Molecule:probable hydrogenase nickel incorporation
PDBTitle: crystal structure of hypb from methanocaldococcus2 jannaschii in the triphosphate form

Phyre2
5 |
| c2wsmB_ |

### PDB 2wsm chain B

Region: 2 - 186
Aligned: 146
Modelled: 168
Confidence: 99.4%
Identity: 24%
PDB header:metal binding protein
Chain: B: PDB Molecule:hydrogenase expression/formation protein (hypb);
PDBTitle: crystal structure of hydrogenase maturation factor hypb from2 archaeoglobus fulgidus

Phyre2
6 |
| c3nxsA_ |

### PDB 3nxs chain A

Region: 3 - 172
Aligned: 145
Modelled: 170
Confidence: 99.3%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:lao/ao transport system atpase;
PDBTitle: crystal structure of lao/ao transport system from mycobacterium2 smegmatis bound to gdp

Phyre2
7 |
| c3dm5A_ |

### PDB 3dm5 chain A

Region: 6 - 185
Aligned: 167
Modelled: 180
Confidence: 99.3%
Identity: 17%
PDB header:rna binding protein, transport protein
Chain: A: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: structures of srp54 and srp19, the two proteins assembling2 the ribonucleic core of the signal recognition particle3 from the archaeon pyrococcus furiosus.

Phyre2
8 |
| d2qm8a1 |

### PDB 2qm8 chain A domain 1

Region: 3 - 176
Aligned: 148
Modelled: 174
Confidence: 99.3%
Identity: 20%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Nitrogenase iron protein-like

Phyre2
9 |
| d1yrba1 |

### PDB 1yrb chain A domain 1

Region: 6 - 186
Aligned: 177
Modelled: 181
Confidence: 99.3%
Identity: 22%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Nitrogenase iron protein-like

Phyre2
10 |
| c3dmdA_ |

### PDB 3dmd chain A

Region: 6 - 189
Aligned: 169
Modelled: 184
Confidence: 99.2%
Identity: 21%
PDB header:transport protein
Chain: A: PDB Molecule:signal recognition particle receptor;
PDBTitle: structures and conformations in solution of the signal recognition2 particle receptor from the archaeon pyrococcus furiosus

Phyre2
11 |
| c2iy3A_ |

### PDB 2iy3 chain A

Region: 2 - 177
Aligned: 163
Modelled: 173
Confidence: 99.2%
Identity: 16%
PDB header:rna-binding
Chain: A: PDB Molecule:signal recognition particle protein ffh;
PDBTitle: structure of the e. coli signal recognition particle2 bound to a translating ribosome

Phyre2
12 |
| c2cnwF_ |

### PDB 2cnw chain F

Region: 2 - 189
Aligned: 176
Modelled: 188
Confidence: 99.2%
Identity: 17%
PDB header:signal recognition
Chain: F: PDB Molecule:cell division protein ftsy;
PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy

Phyre2
13 |
| d1qzxa3 |

### PDB 1qzx chain A domain 3

Region: 6 - 185
Aligned: 173
Modelled: 180
Confidence: 99.2%
Identity: 16%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Nitrogenase iron protein-like

Phyre2
14 |
| c2yhsA_ |

### PDB 2yhs chain A

Region: 2 - 185
Aligned: 174
Modelled: 184
Confidence: 99.2%
Identity: 17%
PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the e. coli srp receptor ftsy

Phyre2
15 |
| c1zu4A_ |

### PDB 1zu4 chain A

Region: 2 - 185
Aligned: 177
Modelled: 184
Confidence: 99.1%
Identity: 19%
PDB header:protein transport
Chain: A: PDB Molecule:ftsy;
PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212

Phyre2
16 |
| c2v3cC_ |

### PDB 2v3c chain C

Region: 2 - 185
Aligned: 171
Modelled: 184
Confidence: 99.1%
Identity: 20%
PDB header:signaling protein
Chain: C: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: crystal structure of the srp54-srp19-7s.s srp rna complex2 of m. jannaschii

Phyre2
17 |
| c2j37W_ |

### PDB 2j37 chain W

Region: 6 - 185
Aligned: 167
Modelled: 180
Confidence: 99.1%
Identity: 14%
PDB header:ribosome
Chain: W: PDB Molecule:signal recognition particle 54 kda protein
PDBTitle: model of mammalian srp bound to 80s rncs

Phyre2
18 |
| c2j7pA_ |

### PDB 2j7p chain A

Region: 6 - 195
Aligned: 175
Modelled: 190
Confidence: 99.1%
Identity: 16%
PDB header:signal recognition
Chain: A: PDB Molecule:signal recognition particle protein;
PDBTitle: gmppnp-stabilized ng domain complex of the srp gtpases ffh2 and ftsy

Phyre2
19 |
| c2f1rA_ |

### PDB 2f1r chain A

Region: 6 - 104
Aligned: 92
Modelled: 99
Confidence: 99.1%
Identity: 17%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:molybdopterin-guanine dinucleotide biosynthesis
PDBTitle: crystal structure of molybdopterin-guanine biosynthesis2 protein b (mobb)

Phyre2
20 |
| c2qy9A_ |

### PDB 2qy9 chain A

Region: 1 - 185
Aligned: 175
Modelled: 185
Confidence: 99.0%
Identity: 18%
PDB header:protein transport
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the ng+1 construct of the e. coli srp receptor2 ftsy

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1nijA_ |
|  | 100.0 | 100 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein yjia; PDBTitle: yjia protein
2 | d1nija1 |
|  | 100.0 | 100 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
3 | d1nija2 |
|  | 99.9 | 100 | Fold:Hypothetical protein YjiA, C-terminal domain Superfamily:Hypothetical protein YjiA, C-terminal domain Family:Hypothetical protein YjiA, C-terminal domain
4 | c2hf9A_ |
|  | 99.5 | 25 | PDB header:hydrolase, metal binding protein Chain: A: PDB Molecule:probable hydrogenase nickel incorporation PDBTitle: crystal structure of hypb from methanocaldococcus2 jannaschii in the triphosphate form
5 | c2wsmB_ |
|  | 99.4 | 24 | PDB header:metal binding protein Chain: B: PDB Molecule:hydrogenase expression/formation protein (hypb); PDBTitle: crystal structure of hydrogenase maturation factor hypb from2 archaeoglobus fulgidus
6 | c3nxsA_ |
|  | 99.3 | 17 | PDB header:transport protein Chain: A: PDB Molecule:lao/ao transport system atpase; PDBTitle: crystal structure of lao/ao transport system from mycobacterium2 smegmatis bound to gdp
7 | c3dm5A_ |
|  | 99.3 | 17 | PDB header:rna binding protein, transport protein Chain: A: PDB Molecule:signal recognition 54 kda protein; PDBTitle: structures of srp54 and srp19, the two proteins assembling2 the ribonucleic core of the signal recognition particle3 from the archaeon pyrococcus furiosus.
8 | d2qm8a1 |
|  | 99.3 | 20 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
9 | d1yrba1 |
|  | 99.3 | 22 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
10 | c3dmdA_ |
|  | 99.2 | 21 | PDB header:transport protein Chain: A: PDB Molecule:signal recognition particle receptor; PDBTitle: structures and conformations in solution of the signal recognition2 particle receptor from the archaeon pyrococcus furiosus
11 | c2iy3A_ |
|  | 99.2 | 16 | PDB header:rna-binding Chain: A: PDB Molecule:signal recognition particle protein ffh; PDBTitle: structure of the e. coli signal recognition particle2 bound to a translating ribosome
12 | c2cnwF_ |
|  | 99.2 | 17 | PDB header:signal recognition Chain: F: PDB Molecule:cell division protein ftsy; PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy
13 | d1qzxa3 |
|  | 99.2 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
14 | c2yhsA_ |
|  | 99.2 | 17 | PDB header:cell cycle Chain: A: PDB Molecule:cell division protein ftsy; PDBTitle: structure of the e. coli srp receptor ftsy
15 | c1zu4A_ |
|  | 99.1 | 19 | PDB header:protein transport Chain: A: PDB Molecule:ftsy; PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212
16 | c2v3cC_ |
|  | 99.1 | 20 | PDB header:signaling protein Chain: C: PDB Molecule:signal recognition 54 kda protein; PDBTitle: crystal structure of the srp54-srp19-7s.s srp rna complex2 of m. jannaschii
17 | c2j37W_ |
|  | 99.1 | 14 | PDB header:ribosome Chain: W: PDB Molecule:signal recognition particle 54 kda protein PDBTitle: model of mammalian srp bound to 80s rncs
18 | c2j7pA_ |
|  | 99.1 | 16 | PDB header:signal recognition Chain: A: PDB Molecule:signal recognition particle protein; PDBTitle: gmppnp-stabilized ng domain complex of the srp gtpases ffh2 and ftsy
19 | c2f1rA_ |
|  | 99.1 | 17 | PDB header:biosynthetic protein Chain: A: PDB Molecule:molybdopterin-guanine dinucleotide biosynthesis PDBTitle: crystal structure of molybdopterin-guanine biosynthesis2 protein b (mobb)
20 | c2qy9A_ |
|  | 99.0 | 18 | PDB header:protein transport Chain: A: PDB Molecule:cell division protein ftsy; PDBTitle: structure of the ng+1 construct of the e. coli srp receptor2 ftsy
21 | c1vmaA_ |
| not modelled | 99.0 | 15 | PDB header:protein transport Chain: A: PDB Molecule:cell division protein ftsy; PDBTitle: crystal structure of cell division protein ftsy (tm0570) from2 thermotoga maritima at 1.60 a resolution
22 | c3b9qA_ |
| not modelled | 99.0 | 14 | PDB header:protein transport Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana
23 | d1ls1a2 |
| not modelled | 99.0 | 15 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
24 | c2og2A_ |
| not modelled | 99.0 | 16 | PDB header:protein transport Chain: A: PDB Molecule:putative signal recognition particle receptor; PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana
25 | c1qzwC_ |
| not modelled | 98.9 | 18 | PDB header:signaling protein/rna Chain: C: PDB Molecule:signal recognition 54 kda protein; PDBTitle: crystal structure of the complete core of archaeal srp and2 implications for inter-domain communication
26 | c2j289_ |
| not modelled | 98.9 | 18 | PDB header:ribosome Chain: 9: PDB Molecule:signal recognition particle 54; PDBTitle: model of e. coli srp bound to 70s rncs
27 | d1vmaa2 |
| not modelled | 98.9 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
28 | c3md0A_ |
| not modelled | 98.8 | 21 | PDB header:transport protein Chain: A: PDB Molecule:arginine/ornithine transport system atpase; PDBTitle: crystal structure of arginine/ornithine transport system2 atpase from mycobacterium tuberculosis bound to gdp (a ras-3 like gtpase superfamily protein)
29 | d2p67a1 |
| not modelled | 98.7 | 23 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
30 | d2qy9a2 |
| not modelled | 98.7 | 17 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
31 | c2wwwB_ |
| not modelled | 98.7 | 22 | PDB header:transport protein Chain: B: PDB Molecule:methylmalonic aciduria type a protein, PDBTitle: crystal structure of methylmalonic acidemia type a protein
32 | c2px0D_ |
| not modelled | 98.6 | 21 | PDB header:biosynthetic protein Chain: D: PDB Molecule:flagellar biosynthesis protein flhf; PDBTitle: crystal structure of flhf complexed with gmppnp/mg(2+)
33 | d1okkd2 |
| not modelled | 98.5 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
34 | c1wf3A_ |
| not modelled | 98.4 | 20 | PDB header:hydrolase Chain: A: PDB Molecule:gtp-binding protein; PDBTitle: crystal structure of gtp-binding protein tt1341 from thermus2 thermophilus hb8
35 | d1xjca_ |
| not modelled | 98.3 | 17 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
36 | c1egaB_ |
| not modelled | 98.3 | 16 | PDB header:hydrolase Chain: B: PDB Molecule:protein (gtp-binding protein era); PDBTitle: crystal structure of a widely conserved gtpase era
37 | c2e87A_ |
| not modelled | 98.3 | 20 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ph1320; PDBTitle: crystal structure of hypothetical gtp-binding protein ph1320 from2 pyrococcus horikoshii ot3, in complex with gdp
38 | c2qptA_ |
| not modelled | 98.3 | 20 | PDB header:endocytosis Chain: A: PDB Molecule:eh domain-containing protein-2; PDBTitle: crystal structure of an ehd atpase involved in membrane remodelling
39 | c2qthA_ |
| not modelled | 98.2 | 17 | PDB header:nucleotide binding protein Chain: A: PDB Molecule:gtp-binding protein; PDBTitle: crystal structure of a gtp-binding protein from the2 hyperthermophilic archaeon sulfolobus solfataricus in3 complex with gdp
40 | c2gedB_ |
| not modelled | 98.2 | 17 | PDB header:protein transport, signaling protein Chain: B: PDB Molecule:signal recognition particle receptor beta PDBTitle: signal recognition particle receptor beta-subunit in2 nucleotide-free dimerized form
41 | c1j8yF_ |
| not modelled | 98.0 | 14 | PDB header:signaling protein Chain: F: PDB Molecule:signal recognition 54 kda protein; PDBTitle: signal recognition particle conserved gtpase domain from a.2 ambivalens t112a mutant
42 | c3k53B_ |
| not modelled | 98.0 | 16 | PDB header:metal transport Chain: B: PDB Molecule:ferrous iron transport protein b; PDBTitle: crystal structure of nfeob from p. furiosus
43 | c3i8sC_ |
| not modelled | 97.9 | 25 | PDB header:transport protein Chain: C: PDB Molecule:ferrous iron transport protein b; PDBTitle: structure of the cytosolic domain of e. coli feob, nucleotide-free2 form
44 | c1wb1C_ |
| not modelled | 97.9 | 20 | PDB header:protein synthesis Chain: C: PDB Molecule:translation elongation factor selb; PDBTitle: crystal structure of translation elongation factor selb2 from methanococcus maripaludis in complex with gdp
45 | c2gzaB_ |
| not modelled | 97.9 | 19 | PDB header:hydrolase Chain: B: PDB Molecule:type iv secretion system protein virb11; PDBTitle: crystal structure of the virb11 atpase from the brucella suis type iv2 secretion system in complex with sulphate
46 | d1g6oa_ |
| not modelled | 97.9 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain)
47 | d1j8yf2 |
| not modelled | 97.8 | 13 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
48 | c1xzqA_ |
| not modelled | 97.8 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:probable trna modification gtpase trme; PDBTitle: structure of the gtp-binding protein trme from thermotoga2 maritima complexed with 5-formyl-thf
49 | c3ievA_ |
| not modelled | 97.8 | 18 | PDB header:nucleotide binding protein/rna Chain: A: PDB Molecule:gtp-binding protein era; PDBTitle: crystal structure of era in complex with mggnp and the 3' end of 16s2 rrna
50 | c3degC_ |
| not modelled | 97.8 | 18 | PDB header:ribosome Chain: C: PDB Molecule:gtp-binding protein lepa; PDBTitle: complex of elongating escherichia coli 70s ribosome and ef4(lepa)-2 gmppnp
51 | c2h5eB_ |
| not modelled | 97.8 | 22 | PDB header:translation Chain: B: PDB Molecule:peptide chain release factor rf-3; PDBTitle: crystal structure of e.coli polypeptide release factor rf3
52 | d1jwyb_ |
| not modelled | 97.7 | 13 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
53 | d1cp2a_ |
| not modelled | 97.7 | 12 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
54 | c2oaq1_ |
| not modelled | 97.7 | 19 | PDB header:hydrolase Chain: 1: PDB Molecule:type ii secretion system protein; PDBTitle: crystal structure of the archaeal secretion atpase gspe in complex2 with phosphate
55 | c3gehA_ |
| not modelled | 97.6 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:trna modification gtpase mnme; PDBTitle: crystal structure of mnme from nostoc in complex with gdp, folinic2 acid and zn
56 | c1g7tA_ |
| not modelled | 97.6 | 20 | PDB header:translation Chain: A: PDB Molecule:translation initiation factor if2/eif5b; PDBTitle: x-ray structure of translation initiation factor if2/eif5b2 complexed with gdpnp
57 | d2dy1a2 |
| not modelled | 97.6 | 21 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
58 | c2hjgA_ |
| not modelled | 97.6 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:gtp-binding protein enga; PDBTitle: the crystal structure of the b. subtilis yphc gtpase in2 complex with gdp
59 | d2bv3a2 |
| not modelled | 97.6 | 22 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
60 | c2qa5A_ |
| not modelled | 97.6 | 14 | PDB header:cell cycle, structural protein Chain: A: PDB Molecule:septin-2; PDBTitle: crystal structure of sept2 g-domain
61 | c3ftqA_ |
| not modelled | 97.6 | 17 | PDB header:cell cycle Chain: A: PDB Molecule:septin-2; PDBTitle: crystal structure of septin 2 in complex with gppnhp and2 mg2+
62 | d1np6a_ |
| not modelled | 97.6 | 28 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
63 | c2bvnB_ |
| not modelled | 97.5 | 20 | PDB header:elongation factor Chain: B: PDB Molecule:elongation factor tu; PDBTitle: e. coli ef-tu:gdpnp in complex with the antibiotic2 enacyloxin iia
64 | d1g3qa_ |
| not modelled | 97.5 | 17 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
65 | c2bm0A_ |
| not modelled | 97.5 | 25 | PDB header:elongation factor Chain: A: PDB Molecule:elongation factor g; PDBTitle: ribosomal elongation factor g (ef-g) fusidic acid resistant2 mutant t84a
66 | c1d2eA_ |
| not modelled | 97.5 | 26 | PDB header:rna binding protein Chain: A: PDB Molecule:elongation factor tu (ef-tu); PDBTitle: crystal structure of mitochondrial ef-tu in complex with gdp
67 | c2ywfA_ |
| not modelled | 97.5 | 16 | PDB header:translation Chain: A: PDB Molecule:gtp-binding protein lepa; PDBTitle: crystal structure of gmppnp-bound lepa from aquifex aeolicus
68 | c3lx8A_ |
| not modelled | 97.5 | 24 | PDB header:metal transport Chain: A: PDB Molecule:ferrous iron uptake transporter protein b; PDBTitle: crystal structure of gdp-bound nfeob from s. thermophilus
69 | c3la6P_ |
| not modelled | 97.5 | 12 | PDB header:transferase Chain: P: PDB Molecule:tyrosine-protein kinase wzc; PDBTitle: octameric kinase domain of the e. coli tyrosine kinase wzc with bound2 adp
70 | c1lnzA_ |
| not modelled | 97.4 | 17 | PDB header:cell cycle Chain: A: PDB Molecule:spo0b-associated gtp-binding protein; PDBTitle: structure of the obg gtp-binding protein
71 | c1mj1A_ |
| not modelled | 97.4 | 18 | PDB header:ribosome Chain: A: PDB Molecule:elongation factor tu; PDBTitle: fitting the ternary complex of ef-tu/trna/gtp and ribosomal proteins2 into a 13 a cryo-em map of the coli 70s ribosome
72 | c2qagC_ |
| not modelled | 97.4 | 16 | PDB header:cell cycle, structural protein Chain: C: PDB Molecule:septin-7; PDBTitle: crystal structure of human septin trimer 2/6/7
73 | d1p9ra_ |
| not modelled | 97.4 | 22 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain)
74 | c3cioA_ |
| not modelled | 97.4 | 13 | PDB header:signaling protein, transferase Chain: A: PDB Molecule:tyrosine-protein kinase etk; PDBTitle: the kinase domain of escherichia coli tyrosine kinase etk
75 | d1rkba_ |
| not modelled | 97.4 | 38 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases
76 | c2xtpA_ |
| not modelled | 97.4 | 15 | PDB header:immune system Chain: A: PDB Molecule:gtpase imap family member 2; PDBTitle: crystal structure of nucleotide-free human gimap2, amino2 acid residues 1-260
77 | c1kk3A_ |
| not modelled | 97.4 | 16 | PDB header:translation Chain: A: PDB Molecule:eif2gamma; PDBTitle: structure of the wild-type large gamma subunit of2 initiation factor eif2 from pyrococcus abyssi complexed3 with gdp-mg2+
78 | c2elfA_ |
| not modelled | 97.4 | 20 | PDB header:translation Chain: A: PDB Molecule:protein translation elongation factor 1a; PDBTitle: crystal structure of the selb-like elongation factor ef-pyl2 from methanosarcina mazei
79 | d1s96a_ |
| not modelled | 97.4 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases
80 | c1skqB_ |
| not modelled | 97.3 | 24 | PDB header:translation Chain: B: PDB Molecule:elongation factor 1-alpha; PDBTitle: the crystal structure of sulfolobus solfataricus elongation2 factor 1-alpha in complex with magnesium and gdp
81 | c3t5dC_ |
| not modelled | 97.3 | 14 | PDB header:signaling protein Chain: C: PDB Molecule:septin-7; PDBTitle: crystal structure of septin 7 in complex with gdp
82 | c1zo1I_ |
| not modelled | 97.3 | 21 | PDB header:translation/rna Chain: I: PDB Molecule:translation initiation factor 2; PDBTitle: if2, if1, and trna fitted to cryo-em data of e. coli 70s2 initiation complex
83 | c2qorA_ |
| not modelled | 97.3 | 16 | PDB header:transferase Chain: A: PDB Molecule:guanylate kinase; PDBTitle: crystal structure of plasmodium vivax guanylate kinase
84 | c3jvvA_ |
| not modelled | 97.3 | 20 | PDB header:atp binding protein Chain: A: PDB Molecule:twitching mobility protein; PDBTitle: crystal structure of p. aeruginosa pilt with bound amp-pcp
85 | c2wjyA_ |
| not modelled | 97.3 | 20 | PDB header:hydrolase Chain: A: PDB Molecule:regulator of nonsense transcripts 1; PDBTitle: crystal structure of the complex between human nonsense2 mediated decay factors upf1 and upf2 orthorhombic form
86 | c2qagB_ |
| not modelled | 97.2 | 25 | PDB header:cell cycle, structural protein Chain: B: PDB Molecule:septin-6; PDBTitle: crystal structure of human septin trimer 2/6/7
87 | d1f60a3 |
| not modelled | 97.2 | 17 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
88 | c2vedA_ |
| not modelled | 97.2 | 15 | PDB header:transferase Chain: A: PDB Molecule:membrane protein capa1, protein tyrosine kinase; PDBTitle: crystal structure of the chimerical mutant capabk55m2 protein
89 | c2j3eA_ |
| not modelled | 97.2 | 16 | PDB header:protein transport Chain: A: PDB Molecule:t7i23.11 protein; PDBTitle: dimerization is important for the gtpase activity of2 chloroplast translocon components attoc33 and pstoc159
90 | c3tr0A_ |
| not modelled | 97.2 | 15 | PDB header:transferase Chain: A: PDB Molecule:guanylate kinase; PDBTitle: structure of guanylate kinase (gmk) from coxiella burnetii
91 | d1nrjb_ |
| not modelled | 97.2 | 17 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
92 | d1egaa1 |
| not modelled | 97.2 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
93 | c3tr5C_ |
| not modelled | 97.2 | 18 | PDB header:translation Chain: C: PDB Molecule:peptide chain release factor 3; PDBTitle: structure of a peptide chain release factor 3 (prfc) from coxiella2 burnetii
94 | c3a1vB_ |
| not modelled | 97.2 | 20 | PDB header:transport protein Chain: B: PDB Molecule:iron(ii) transport protein b; PDBTitle: crystal structue of the cytosolic domain of t. maritima feob2 iron iransporter in apo form
95 | c2xexA_ |
| not modelled | 97.2 | 22 | PDB header:translation Chain: A: PDB Molecule:elongation factor g; PDBTitle: crystal structure of staphylococcus aureus elongation factor2 g
96 | d2afhe1 |
| not modelled | 97.2 | 11 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
97 | d2c78a3 |
| not modelled | 97.2 | 19 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
98 | c3lxxA_ |
| not modelled | 97.2 | 18 | PDB header:immune system Chain: A: PDB Molecule:gtpase imap family member 4; PDBTitle: crystal structure of human gtpase imap family member 4
99 | d1ihua1 |
| not modelled | 97.1 | 14 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
100 | d1h65a_ |
| not modelled | 97.1 | 21 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
101 | c2bwjC_ |
| not modelled | 97.1 | 19 | PDB header:transferase Chain: C: PDB Molecule:adenylate kinase 5; PDBTitle: structure of adenylate kinase 5
102 | c3lxwA_ |
| not modelled | 97.1 | 22 | PDB header:immune system Chain: A: PDB Molecule:gtpase imap family member 1; PDBTitle: crystal structure of human gtpase imap family member 1
103 | c1r5nA_ |
| not modelled | 97.1 | 19 | PDB header:translation Chain: A: PDB Molecule:eukaryotic peptide chain release factor gtp- PDBTitle: crystal structure analysis of sup35 complexed with gdp
104 | c1jalA_ |
| not modelled | 97.1 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ychf protein; PDBTitle: ychf protein (hi0393)
105 | c2vyeA_ |
| not modelled | 97.1 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:replicative dna helicase; PDBTitle: crystal structure of the dnac-ssdna complex
106 | c2ja1A_ |
| not modelled | 97.1 | 15 | PDB header:transferase Chain: A: PDB Molecule:thymidine kinase; PDBTitle: thymidine kinase from b. cereus with ttp bound as phosphate2 donor.
107 | d1g7sa4 |
| not modelled | 97.1 | 37 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
108 | c1ly1A_ |
| not modelled | 97.1 | 28 | PDB header:transferase Chain: A: PDB Molecule:polynucleotide kinase; PDBTitle: structure and mechanism of t4 polynucleotide kinase
109 | d1ly1a_ |
| not modelled | 97.1 | 28 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases
110 | c1mkyA_ |
| not modelled | 97.1 | 20 | PDB header:ligand binding protein Chain: A: PDB Molecule:probable gtp-binding protein enga; PDBTitle: structural analysis of the domain interactions in der, a2 switch protein containing two gtpase domains
111 | d1mo6a1 |
| not modelled | 97.0 | 19 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain)
112 | c2dy1A_ |
| not modelled | 97.0 | 20 | PDB header:signaling protein, translation Chain: A: PDB Molecule:elongation factor g; PDBTitle: crystal structure of ef-g-2 from thermus thermophilus
113 | d1qhxa_ |
| not modelled | 97.0 | 24 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Chloramphenicol phosphotransferase
114 | d1n0ua2 |
| not modelled | 97.0 | 17 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
115 | c3io3A_ |
| not modelled | 97.0 | 10 | PDB header:chaperone Chain: A: PDB Molecule:deha2d07832p; PDBTitle: get3 with adp from d. hansenii in closed form
116 | d3adka_ |
| not modelled | 97.0 | 22 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases
117 | d1ihua2 |
| not modelled | 97.0 | 11 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
118 | d1jnya3 |
| not modelled | 97.0 | 18 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:G proteins
119 | c2qagA_ |
| not modelled | 97.0 | 17 | PDB header:cell cycle, structural protein Chain: A: PDB Molecule:septin-2; PDBTitle: crystal structure of human septin trimer 2/6/7
120 | c3ch4B_ |
| not modelled | 97.0 | 16 | PDB header:transferase Chain: B: PDB Molecule:phosphomevalonate kinase; PDBTitle: the crystal structure of human phosphomavelonate kinase at2 1.8 a resolution

Binding site prediction |

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
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Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0