Phyre 2 Results for P0ABC7

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Email | l.a.kelley@imperial.ac.uk
Description | P0ABC7
Date | Thu Jan 5 11:15:10 GMT 2012
Unique Job ID | f60184711b331ed6

Summary |

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

Model (left) based on template c3bk6C_
Top template information
PDB header:membrane protein Chain: C: PDB Molecule:ph stomatin; PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii
Confidence and coverage
Confidence: | 99.9% | Coverage: | 37%
157 residues ( 37% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
237 residues ( 57%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | A | W | N | Q | P | G | N | N | G | Q | D | R | D | P | W | G | S | S | K | P | G | G | N | S | E | G | N | G | N | K | G | G | R | D | Q | G | P | P | D | L | D | D | I | F | R | K | L | S | K | K | L | G | G | L | G | G | G | K | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | T | G | S | G | G | G | S | S | S | Q | G | P | R | P | Q | L | G | G | R | V | V | T | I | A | A | A | A | I | V | I | I | W | A | A | S | G | F | Y | T | I | K | E | A | E | R | G | V | V | T | R | F | G | K | F | S | H | L | V | E | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | G | L | N | W | K | P | T | F | I | D | E | V | K | P | V | N | V | E | A | V | R | E | L | A | A | S | G | V | M | L | T | S | D | E | N | V | V | R | V | E | M | N | V | Q | Y | R | V | T | N | P | E | K | Y | L | Y | S | V | T | S | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | D | D | S | L | R | Q | A | T | D | S | A | L | R | G | V | I | G | K | Y | T | M | D | R | I | L | T | E | G | R | T | V | I | R | S | D | T | Q | R | E | L | E | E | T | I | R | P | Y | D | M | G | I | T | L | L | D | V | N | F | Q | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | A | R | P | P | E | E | V | K | A | A | F | D | D | A | I | A | A | R | E | N | E | Q | Q | Y | I | R | E | A | E | A | Y | T | N | E | V | Q | P | R | A | N | G | Q | A | Q | R | I | L | E | E | A | R | A | Y | K | A | Q | T | I | L | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | . | . | . | . | . | 360
Sequence |  | A | Q | G | E | V | A | R | F | A | K | L | L | P | E | Y | K | A | A | P | E | I | T | R | E | R | L | Y | I | E | T | M | E | K | V | L | G | N | T | R | K | V | L | V | N | D | K | G | G | N | L | M | V | L | P | L | D | Q | M | L | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  | ? |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 370 | . | . | . | . | . | . | . | . | . | 380 | . | . | . | . | . | . | . | . | . | 390 | . | . | . | . | . | . | . | . | . | 400 | . | . | . | . | . | . | . | . | . | 410 | . | . | . | . | . | . | . | . | .
Sequence |  | G | G | N | A | P | A | A | K | S | D | N | G | A | S | N | L | L | R | L | P | P | A | S | S | S | T | T | S | G | A | S | N | T | S | S | T | S | Q | G | D | I | M | D | Q | R | R | A | N | A | Q | R | N | D | Y | Q | R | Q | G | E
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 |
| c3bk6C_ |

### PDB 3bk6 chain C

Region: 128 - 289
Aligned: 157
Modelled: 162
Confidence: 99.9%
Identity: 25%
PDB header:membrane protein
Chain: C: PDB Molecule:ph stomatin;
PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii

Phyre2
2 |
| c2rpbA_ |

### PDB 2rpb chain A

Region: 134 - 246
Aligned: 110
Modelled: 113
Confidence: 99.8%
Identity: 25%
PDB header:membrane protein
Chain: A: PDB Molecule:hypothetical membrane protein;
PDBTitle: the solution structure of membrane protein

Phyre2
3 |
| d1wina_ |

### PDB 1win chain A

Region: 130 - 257
Aligned: 125
Modelled: 128
Confidence: 99.7%
Identity: 14%
Fold: EF-Ts domain-like
Superfamily: Band 7/SPFH domain
Family: Band 7/SPFH domain

Phyre2
4 |
| c2zv4O_ |

### PDB 2zv4 chain O

Region: 98 - 334
Aligned: 236
Modelled: 237
Confidence: 98.1%
Identity: 20%
PDB header:structural protein
Chain: O: PDB Molecule:major vault protein;
PDBTitle: the structure of rat liver vault at 3.5 angstrom resolution

Phyre2
5 |
| c2kk7A_ |

### PDB 2kk7 chain A

Region: 269 - 307
Aligned: 39
Modelled: 39
Confidence: 80.5%
Identity: 26%
PDB header:hydrolase
Chain: A: PDB Molecule:v-type atp synthase subunit e;
PDBTitle: nmr solution structure of the n terminal domain of subunit e2 (e1-52) of a1ao atp synthase from methanocaldococcus3 jannaschii

Phyre2
6 |
| c2k88A_ |

### PDB 2k88 chain A

Region: 276 - 320
Aligned: 42
Modelled: 45
Confidence: 51.3%
Identity: 29%
PDB header:hydrolase
Chain: A: PDB Molecule:vacuolar proton pump subunit g;
PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase

Phyre2
7 |
| d1l2pa_ |

### PDB 1l2p chain A

Region: 264 - 323
Aligned: 58
Modelled: 60
Confidence: 49.5%
Identity: 28%
Fold: Single transmembrane helix
Superfamily: F1F0 ATP synthase subunit B, membrane domain
Family: F1F0 ATP synthase subunit B, membrane domain

Phyre2
8 |
| c2kepA_ |

### PDB 2kep chain A

Region: 3 - 19
Aligned: 17
Modelled: 17
Confidence: 44.4%
Identity: 41%
PDB header:transport protein
Chain: A: PDB Molecule:general secretion pathway protein g;
PDBTitle: solution structure of xcpt, the main component of the type 22 secretion system of pseudomonas aeruginosa

Phyre2
9 |
| c3k5bE_ |

### PDB 3k5b chain E

Region: 262 - 337
Aligned: 76
Modelled: 76
Confidence: 43.5%
Identity: 13%
PDB header:hydrolase
Chain: E: PDB Molecule:v-type atp synthase subunit e;
PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase

Phyre2
10 |
| c3u5gB_ |

### PDB 3u5g chain B

Region: 141 - 241
Aligned: 95
Modelled: 101
Confidence: 33.8%
Identity: 17%
PDB header:ribosome
Chain: B: PDB Molecule:40s ribosomal protein s1-a;
PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution

Phyre2
11 |
| c1wd6B_ |

### PDB 1wd6 chain B

Region: 119 - 130
Aligned: 12
Modelled: 12
Confidence: 27.9%
Identity: 42%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:protein ydhr;
PDBTitle: crystal structure of jw1657 from escherichia coli

Phyre2
12 |
| d1t92a_ |

### PDB 1t92 chain A

Region: 3 - 19
Aligned: 17
Modelled: 17
Confidence: 25.9%
Identity: 29%
Fold: Pili subunits
Superfamily: Pili subunits
Family: Pseudopilin

Phyre2
13 |
| c2i7uA_ |

### PDB 2i7u chain A

Region: 41 - 65
Aligned: 25
Modelled: 25
Confidence: 25.0%
Identity: 36%
PDB header:de novo protein/ligand binding protein
Chain: A: PDB Molecule:four-alpha-helix bundle;
PDBTitle: structural and dynamical analysis of a four-alpha-helix2 bundle with designed anesthetic binding pockets

Phyre2
14 |
| c3fu1B_ |

### PDB 3fu1 chain B

Region: 3 - 19
Aligned: 17
Modelled: 17
Confidence: 19.2%
Identity: 24%
PDB header:protein transport
Chain: B: PDB Molecule:general secretion pathway protein g;
PDBTitle: crystal structure of the major pseudopilin from the type 2 secretion2 system of vibrio cholerae

Phyre2
15 |
| c2xzm4_ |

### PDB 2xzm chain 4

Region: 141 - 241
Aligned: 95
Modelled: 101
Confidence: 18.9%
Identity: 14%
PDB header:ribosome
Chain: 4: PDB Molecule:40s ribosomal protein s3a;
PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1

Phyre2
16 |
| c2vgpD_ |

### PDB 2vgp chain D

Region: 37 - 45
Aligned: 9
Modelled: 9
Confidence: 12.8%
Identity: 33%
PDB header:transferase
Chain: D: PDB Molecule:inner centromere protein a;
PDBTitle: crystal structure of aurora b kinase in complex with a2 aminothiazole inhibitor

Phyre2
17 |
| d2hiqa1 |

### PDB 2hiq chain A domain 1

Region: 119 - 130
Aligned: 12
Modelled: 12
Confidence: 12.6%
Identity: 42%
Fold: Ferredoxin-like
Superfamily: Dimeric alpha+beta barrel
Family: Hypothetical protein YdhR

Phyre2
18 |
| d1tf5a1 |

### PDB 1tf5 chain A domain 1

Region: 98 - 123
Aligned: 26
Modelled: 26
Confidence: 11.3%
Identity: 23%
Fold: Pre-protein crosslinking domain of SecA
Superfamily: Pre-protein crosslinking domain of SecA
Family: Pre-protein crosslinking domain of SecA

Phyre2
19 |
| c3k5bB_ |

### PDB 3k5b chain B

Region: 263 - 333
Aligned: 68
Modelled: 68
Confidence: 11.0%
Identity: 22%
PDB header:hydrolase
Chain: B: PDB Molecule:v-type atp synthase, subunit (vapc-therm);
PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase

Phyre2
20 |
| c1tt9B_ |

### PDB 1tt9 chain B

Region: 280 - 417
Aligned: 137
Modelled: 138
Confidence: 10.9%
Identity: 14%
PDB header:transferase, lyase
Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase
PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer

Phyre2
21 |
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26 |
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50 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3bk6C_ |
|  | 99.9 | 25 | PDB header:membrane protein Chain: C: PDB Molecule:ph stomatin; PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii
2 | c2rpbA_ |
|  | 99.8 | 25 | PDB header:membrane protein Chain: A: PDB Molecule:hypothetical membrane protein; PDBTitle: the solution structure of membrane protein
3 | d1wina_ |
|  | 99.7 | 14 | Fold:EF-Ts domain-like Superfamily:Band 7/SPFH domain Family:Band 7/SPFH domain
4 | c2zv4O_ |
|  | 98.1 | 20 | PDB header:structural protein Chain: O: PDB Molecule:major vault protein; PDBTitle: the structure of rat liver vault at 3.5 angstrom resolution
5 | c2kk7A_ |
|  | 80.5 | 26 | PDB header:hydrolase Chain: A: PDB Molecule:v-type atp synthase subunit e; PDBTitle: nmr solution structure of the n terminal domain of subunit e2 (e1-52) of a1ao atp synthase from methanocaldococcus3 jannaschii
6 | c2k88A_ |
|  | 51.3 | 29 | PDB header:hydrolase Chain: A: PDB Molecule:vacuolar proton pump subunit g; PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase
7 | d1l2pa_ |
|  | 49.5 | 28 | Fold:Single transmembrane helix Superfamily:F1F0 ATP synthase subunit B, membrane domain Family:F1F0 ATP synthase subunit B, membrane domain
8 | c2kepA_ |
|  | 44.4 | 41 | PDB header:transport protein Chain: A: PDB Molecule:general secretion pathway protein g; PDBTitle: solution structure of xcpt, the main component of the type 22 secretion system of pseudomonas aeruginosa
9 | c3k5bE_ |
|  | 43.5 | 13 | PDB header:hydrolase Chain: E: PDB Molecule:v-type atp synthase subunit e; PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase
10 | c3u5gB_ |
|  | 33.8 | 17 | PDB header:ribosome Chain: B: PDB Molecule:40s ribosomal protein s1-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution
11 | c1wd6B_ |
|  | 27.9 | 42 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli
12 | d1t92a_ |
|  | 25.9 | 29 | Fold:Pili subunits Superfamily:Pili subunits Family:Pseudopilin
13 | c2i7uA_ |
|  | 25.0 | 36 | PDB header:de novo protein/ligand binding protein Chain: A: PDB Molecule:four-alpha-helix bundle; PDBTitle: structural and dynamical analysis of a four-alpha-helix2 bundle with designed anesthetic binding pockets
14 | c3fu1B_ |
|  | 19.2 | 24 | PDB header:protein transport Chain: B: PDB Molecule:general secretion pathway protein g; PDBTitle: crystal structure of the major pseudopilin from the type 2 secretion2 system of vibrio cholerae
15 | c2xzm4_ |
|  | 18.9 | 14 | PDB header:ribosome Chain: 4: PDB Molecule:40s ribosomal protein s3a; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1
16 | c2vgpD_ |
|  | 12.8 | 33 | PDB header:transferase Chain: D: PDB Molecule:inner centromere protein a; PDBTitle: crystal structure of aurora b kinase in complex with a2 aminothiazole inhibitor
17 | d2hiqa1 |
|  | 12.6 | 42 | Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Hypothetical protein YdhR
18 | d1tf5a1 |
|  | 11.3 | 23 | Fold:Pre-protein crosslinking domain of SecA Superfamily:Pre-protein crosslinking domain of SecA Family:Pre-protein crosslinking domain of SecA
19 | c3k5bB_ |
|  | 11.0 | 22 | PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase, subunit (vapc-therm); PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase
20 | c1tt9B_ |
|  | 10.9 | 14 | PDB header:transferase, lyase Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer
21 | c3kdpD_ |
| not modelled | 10.5 | 18 | PDB header:hydrolase Chain: D: PDB Molecule:sodium/potassium-transporting atpase subunit beta-1; PDBTitle: crystal structure of the sodium-potassium pump
22 | d1htjf_ |
| not modelled | 9.1 | 15 | Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS
23 | c1htjF_ |
| not modelled | 9.1 | 15 | PDB header:signaling protein Chain: F: PDB Molecule:kiaa0380; PDBTitle: structure of the rgs-like domain from pdz-rhogef
24 | c3swfA_ |
| not modelled | 8.2 | 40 | PDB header:transport protein Chain: A: PDB Molecule:cgmp-gated cation channel alpha-1; PDBTitle: cnga1 621-690 containing clz domain
25 | d5ruba2 |
| not modelled | 7.3 | 25 | Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase
26 | c1jsuC_ |
| not modelled | 7.1 | 32 | PDB header:complex (transferase/cyclin/inhibitor) Chain: C: PDB Molecule:p27; PDBTitle: p27(kip1)/cyclin a/cdk2 complex
27 | c2w2hD_ |
| not modelled | 6.8 | 32 | PDB header:rna-binding protein Chain: D: PDB Molecule:protein tat; PDBTitle: structural basis of transcription activation by the cyclin2 t1-tat-tar rna complex from eiav
28 | d1wuua1 |
| not modelled | 6.8 | 10 | Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:GHMP Kinase, N-terminal domain
29 | c3s93B_ |
| not modelled | 6.5 | 11 | PDB header:transcription Chain: B: PDB Molecule:tudor domain-containing protein 5; PDBTitle: crystal structure of conserved motif in tdrd5
30 | d1wmda1 |
| not modelled | 6.4 | 11 | Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Proprotein convertase P-domain
31 | c2jp3A_ |
| not modelled | 6.4 | 36 | PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles
32 | c2ptmA_ |
| not modelled | 6.4 | 10 | PDB header:transport protein Chain: A: PDB Molecule:hyperpolarization-activated (ih) channel; PDBTitle: structure and rearrangements in the carboxy-terminal region of spih2 channels
33 | c2jo1A_ |
| not modelled | 6.3 | 24 | PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles
34 | d2o4ta1 |
| not modelled | 6.3 | 6 | Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like
35 | d1o5ha_ |
| not modelled | 6.1 | 19 | Fold:Methenyltetrahydrofolate cyclohydrolase-like Superfamily:Methenyltetrahydrofolate cyclohydrolase-like Family:Methenyltetrahydrofolate cyclohydrolase-like
36 | d2ozla1 |
| not modelled | 6.0 | 20 | Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:Branched-chain alpha-keto acid dehydrogenase PP module
37 | c1y4cA_ |
| not modelled | 5.8 | 15 | PDB header:de novo protein Chain: A: PDB Molecule:maltose binding protein fused with designed PDBTitle: designed helical protein fusion mbp
38 | c2kncB_ |
| not modelled | 5.7 | 13 | PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
39 | d1fftb2 |
| not modelled | 5.7 | 7 | Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region
40 | d1nkta1 |
| not modelled | 5.5 | 14 | Fold:Pre-protein crosslinking domain of SecA Superfamily:Pre-protein crosslinking domain of SecA Family:Pre-protein crosslinking domain of SecA
41 | c1o7fA_ |
| not modelled | 5.5 | 17 | PDB header:regulation Chain: A: PDB Molecule:camp-dependent rap1 guanine-nucleotide exchange PDBTitle: crystal structure of the regulatory domain of epac2
42 | c2k6iA_ |
| not modelled | 5.5 | 34 | PDB header:structural protein Chain: A: PDB Molecule:uncharacterized protein mj0223; PDBTitle: the domain features of the peripheral stalk subunit h of the2 methanogenic a1ao atp synthase and the nmr solution3 structure of h1-47
43 | c2zxeB_ |
| not modelled | 5.4 | 21 | PDB header:hydrolase/transport protein Chain: B: PDB Molecule:na+,k+-atpase beta subunit; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state
44 | d1ykwa2 |
| not modelled | 5.4 | 21 | Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase
45 | c3nngA_ |
| not modelled | 5.3 | 21 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the f5/8 type c domain of q5lfr2_bacfn protein2 from bacteroides fragilis. northeast structural genomics consortium3 target bfr258e
46 | d1e3pa2 |
| not modelled | 5.3 | 39 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
47 | c9paiB_ |
| not modelled | 5.3 | 15 | PDB header:hydrolase inhibitor Chain: B: PDB Molecule:protein (plasminogen activator inhibitor-1) residues 365- PDBTitle: cleaved substrate variant of plasminogen activator inhibitor-1
48 | c2axcA_ |
| not modelled | 5.3 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:colicin e7; PDBTitle: crystal structure of cole7 translocation domain
49 | c3i24B_ |
| not modelled | 5.1 | 17 | PDB header:hydrolase Chain: B: PDB Molecule:hit family hydrolase; PDBTitle: crystal structure of a hit family hydrolase protein from2 vibrio fischeri. northeast structural genomics consortium3 target id vfr176
50 | d2hsga1 |
| not modelled | 5.1 | 21 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator

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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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