Phyre 2 Results for P0AAT4

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P0AAT4
Date | Thu Jan 5 11:13:46 GMT 2012
Unique Job ID | c7fa664ad6996e65

Summary |

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

Model (left) based on template c2vv5D_
Top template information
PDB header:membrane protein Chain: D: PDB Molecule:small-conductance mechanosensitive channel; PDBTitle: the open structure of mscs
Confidence and coverage
Confidence: | 100.0% | Coverage: | 59%
244 residues ( 59% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | Q | D | L | I | S | Q | V | E | D | L | A | G | I | E | I | D | H | T | T | S | M | V | M | I | F | G | I | I | F | L | T | A | V | V | V | H | I | I | L | H | W | V | V | L | R | T | F | E | K | R | A | I | A | S | S | R | L | W | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | I | I | T | Q | N | K | L | F | H | R | L | A | F | T | L | Q | G | I | I | V | N | I | Q | A | V | F | W | L | Q | K | G | T | E | A | A | D | I | L | T | T | C | A | Q | L | W | I | M | M | Y | A | L | L | S | V | F | S | L | L | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | V | I | L | N | L | A | Q | K | F | P | A | A | S | Q | L | P | L | K | G | I | F | Q | G | I | K | L | I | G | A | I | L | V | G | I | L | M | I | S | L | L | I | G | Q | S | P | A | I | L | I | S | G | L | G | A | M | A | A | V | L | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | L | V | F | K | D | P | I | L | G | L | V | A | G | I | Q | L | S | A | N | D | M | L | K | L | G | D | W | L | E | M | P | K | Y | G | A | D | G | A | V | I | D | I | G | L | T | T | V | K | V | R | N | W | D | N | T | I | T | T | I | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | T | W | S | L | V | S | D | S | F | K | N | W | S | G | M | S | A | S | G | G | R | R | I | K | R | S | I | S | I | D | V | T | S | I | R | F | L | D | E | D | E | M | Q | R | L | N | K | A | H | L | L | K | P | Y | L | T | S | R | H | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  | ? |  | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  | ? | ? |  | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | . | . | . | . | . | 360
Sequence |  | E | I | N | E | W | N | R | Q | Q | G | S | T | E | S | V | L | N | L | R | R | M | T | N | I | G | T | F | R | A | Y | L | N | E | Y | L | R | N | H | P | R | I | R | K | D | M | T | L | M | V | R | Q | L | A | P | G | D | N | G | L | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 370 | . | . | . | . | . | . | . | . | . | 380 | . | . | . | . | . | . | . | . | . | 390 | . | . | . | . | . | . | . | . | . | 400 | . | . | . | . | . | . | . | . | . | 410 | . | . | . | . | .
Sequence |  | L | E | I | Y | A | F | T | N | T | V | V | W | L | E | Y | E | S | I | Q | A | D | I | F | D | H | I | F | A | I | V | E | E | F | G | L | R | L | H | Q | S | P | T | G | N | D | I | R | S | L | A | G | A | F | K | Q
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 |
| c2vv5D_ |

### PDB 2vv5 chain D

Region: 101 - 403
Aligned: 244
Modelled: 252
Confidence: 100.0%
Identity: 18%
PDB header:membrane protein
Chain: D: PDB Molecule:small-conductance mechanosensitive channel;
PDBTitle: the open structure of mscs

Phyre2
2 |
| d2vv5a1 |

### PDB 2vv5 chain A domain 1

Region: 186 - 253
Aligned: 66
Modelled: 66
Confidence: 99.8%
Identity: 23%
Fold: Sm-like fold
Superfamily: Sm-like ribonucleoproteins
Family: Mechanosensitive channel protein MscS (YggB), middle domain

Phyre2
3 |
| d2vv5a2 |

### PDB 2vv5 chain A domain 2

Region: 257 - 402
Aligned: 93
Modelled: 97
Confidence: 99.2%
Identity: 19%
Fold: Ferredoxin-like
Superfamily: Mechanosensitive channel protein MscS (YggB), C-terminal domain
Family: Mechanosensitive channel protein MscS (YggB), C-terminal domain

Phyre2
4 |
| d2vv5a3 |

### PDB 2vv5 chain A domain 3

Region: 101 - 184
Aligned: 83
Modelled: 84
Confidence: 98.7%
Identity: 14%
Fold: Mechanosensitive channel protein MscS (YggB), transmembrane region
Superfamily: Mechanosensitive channel protein MscS (YggB), transmembrane region
Family: Mechanosensitive channel protein MscS (YggB), transmembrane region

Phyre2
5 |
| d1nz9a_ |

### PDB 1nz9 chain A

Region: 201 - 223
Aligned: 23
Modelled: 23
Confidence: 80.7%
Identity: 22%
Fold: SH3-like barrel
Superfamily: Translation proteins SH3-like domain
Family: N-utilization substance G protein NusG, C-terminal domain

Phyre2
6 |
| d1nppa2 |

### PDB 1npp chain A domain 2

Region: 201 - 223
Aligned: 23
Modelled: 23
Confidence: 78.9%
Identity: 17%
Fold: SH3-like barrel
Superfamily: Translation proteins SH3-like domain
Family: N-utilization substance G protein NusG, C-terminal domain

Phyre2
7 |
| d2hqha1 |

### PDB 2hqh chain A domain 1

Region: 201 - 223
Aligned: 23
Modelled: 23
Confidence: 78.6%
Identity: 30%
Fold: SH3-like barrel
Superfamily: Cap-Gly domain
Family: Cap-Gly domain

Phyre2
8 |
| c2kvqG_ |

### PDB 2kvq chain G

Region: 201 - 223
Aligned: 23
Modelled: 23
Confidence: 76.8%
Identity: 13%
PDB header:transcription
Chain: G: PDB Molecule:transcription antitermination protein nusg;
PDBTitle: solution structure of nuse:nusg-ctd complex

Phyre2
9 |
| c2jvvA_ |

### PDB 2jvv chain A

Region: 201 - 223
Aligned: 23
Modelled: 23
Confidence: 76.8%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:transcription antitermination protein nusg;
PDBTitle: solution structure of e. coli nusg carboxyterminal domain

Phyre2
10 |
| c2e6zA_ |

### PDB 2e6z chain A

Region: 199 - 244
Aligned: 46
Modelled: 46
Confidence: 74.6%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt5;
PDBTitle: solution structure of the second kow motif of human2 transcription elongation factor spt5

Phyre2
11 |
| c2zkrt_ |

### PDB 2zkr chain T

Region: 201 - 240
Aligned: 40
Modelled: 40
Confidence: 70.4%
Identity: 13%
PDB header:ribosomal protein/rna
Chain: T: PDB Molecule:rna expansion segment es39 part iii;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map

Phyre2
12 |
| c2l82A_ |

### PDB 2l82 chain A

Region: 266 - 398
Aligned: 105
Modelled: 115
Confidence: 69.5%
Identity: 16%
PDB header:de novo protein
Chain: A: PDB Molecule:designed protein or32;
PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or32

Phyre2
13 |
| d1t9ha1 |

### PDB 1t9h chain A domain 1

Region: 204 - 226
Aligned: 23
Modelled: 23
Confidence: 63.1%
Identity: 22%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2
14 |
| c3p8bB_ |

### PDB 3p8b chain B

Region: 201 - 223
Aligned: 23
Modelled: 23
Confidence: 61.1%
Identity: 30%
PDB header:transferase/transcription
Chain: B: PDB Molecule:transcription antitermination protein nusg;
PDBTitle: x-ray crystal structure of pyrococcus furiosus transcription2 elongation factor spt4/5

Phyre2
15 |
| d1u0la1 |

### PDB 1u0l chain A domain 1

Region: 201 - 222
Aligned: 22
Modelled: 22
Confidence: 60.0%
Identity: 23%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2
16 |
| c2rcnA_ |

### PDB 2rcn chain A

Region: 200 - 230
Aligned: 31
Modelled: 31
Confidence: 59.5%
Identity: 19%
PDB header:hydrolase
Chain: A: PDB Molecule:probable gtpase engc;
PDBTitle: crystal structure of the ribosomal interacting gtpase yjeq from the2 enterobacterial species salmonella typhimurium.

Phyre2
17 |
| d2gvha1 |

### PDB 2gvh chain A domain 1

Region: 198 - 230
Aligned: 28
Modelled: 33
Confidence: 56.7%
Identity: 14%
Fold: Thioesterase/thiol ester dehydrase-isomerase
Superfamily: Thioesterase/thiol ester dehydrase-isomerase
Family: 4HBT-like

Phyre2
18 |
| c2gvhC_ |

### PDB 2gvh chain C

Region: 198 - 230
Aligned: 28
Modelled: 29
Confidence: 54.3%
Identity: 18%
PDB header:hydrolase
Chain: C: PDB Molecule:agr_l_2016p;
PDBTitle: crystal structure of acyl-coa hydrolase (15159470) from agrobacterium2 tumefaciens at 2.65 a resolution

Phyre2
19 |
| d2eyqa1 |

### PDB 2eyq chain A domain 1

Region: 195 - 244
Aligned: 49
Modelled: 50
Confidence: 53.7%
Identity: 16%
Fold: SH3-like barrel
Superfamily: CarD-like
Family: CarD-like

Phyre2
20 |
| c2yv5A_ |

### PDB 2yv5 chain A

Region: 199 - 240
Aligned: 42
Modelled: 42
Confidence: 52.5%
Identity: 17%
PDB header:hydrolase
Chain: A: PDB Molecule:yjeq protein;
PDBTitle: crystal structure of yjeq from aquifex aeolicus

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2vv5D_ |
|  | 100.0 | 18 | PDB header:membrane protein Chain: D: PDB Molecule:small-conductance mechanosensitive channel; PDBTitle: the open structure of mscs
2 | d2vv5a1 |
|  | 99.8 | 23 | Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Mechanosensitive channel protein MscS (YggB), middle domain
3 | d2vv5a2 |
|  | 99.2 | 19 | Fold:Ferredoxin-like Superfamily:Mechanosensitive channel protein MscS (YggB), C-terminal domain Family:Mechanosensitive channel protein MscS (YggB), C-terminal domain
4 | d2vv5a3 |
|  | 98.7 | 14 | Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region
5 | d1nz9a_ |
|  | 80.7 | 22 | Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:N-utilization substance G protein NusG, C-terminal domain
6 | d1nppa2 |
|  | 78.9 | 17 | Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:N-utilization substance G protein NusG, C-terminal domain
7 | d2hqha1 |
|  | 78.6 | 30 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
8 | c2kvqG_ |
|  | 76.8 | 13 | PDB header:transcription Chain: G: PDB Molecule:transcription antitermination protein nusg; PDBTitle: solution structure of nuse:nusg-ctd complex
9 | c2jvvA_ |
|  | 76.8 | 13 | PDB header:transcription Chain: A: PDB Molecule:transcription antitermination protein nusg; PDBTitle: solution structure of e. coli nusg carboxyterminal domain
10 | c2e6zA_ |
|  | 74.6 | 13 | PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt5; PDBTitle: solution structure of the second kow motif of human2 transcription elongation factor spt5
11 | c2zkrt_ |
|  | 70.4 | 13 | PDB header:ribosomal protein/rna Chain: T: PDB Molecule:rna expansion segment es39 part iii; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
12 | c2l82A_ |
|  | 69.5 | 16 | PDB header:de novo protein Chain: A: PDB Molecule:designed protein or32; PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or32
13 | d1t9ha1 |
|  | 63.1 | 22 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
14 | c3p8bB_ |
|  | 61.1 | 30 | PDB header:transferase/transcription Chain: B: PDB Molecule:transcription antitermination protein nusg; PDBTitle: x-ray crystal structure of pyrococcus furiosus transcription2 elongation factor spt4/5
15 | d1u0la1 |
|  | 60.0 | 23 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
16 | c2rcnA_ |
|  | 59.5 | 19 | PDB header:hydrolase Chain: A: PDB Molecule:probable gtpase engc; PDBTitle: crystal structure of the ribosomal interacting gtpase yjeq from the2 enterobacterial species salmonella typhimurium.
17 | d2gvha1 |
|  | 56.7 | 14 | Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:4HBT-like
18 | c2gvhC_ |
|  | 54.3 | 18 | PDB header:hydrolase Chain: C: PDB Molecule:agr_l_2016p; PDBTitle: crystal structure of acyl-coa hydrolase (15159470) from agrobacterium2 tumefaciens at 2.65 a resolution
19 | d2eyqa1 |
|  | 53.7 | 16 | Fold:SH3-like barrel Superfamily:CarD-like Family:CarD-like
20 | c2yv5A_ |
|  | 52.5 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:yjeq protein; PDBTitle: crystal structure of yjeq from aquifex aeolicus
21 | d1whka_ |
| not modelled | 52.5 | 16 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
22 | d1whma_ |
| not modelled | 51.6 | 16 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
23 | d1y7ua1 |
| not modelled | 50.9 | 25 | Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:4HBT-like
24 | c1t9hA_ |
| not modelled | 50.7 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:probable gtpase engc; PDBTitle: the crystal structure of yloq, a circularly permuted gtpase.
25 | c3b7kA_ |
| not modelled | 50.3 | 25 | PDB header:hydrolase Chain: A: PDB Molecule:acyl-coenzyme a thioesterase 12; PDBTitle: human acyl-coenzyme a thioesterase 12
26 | d2gvha2 |
| not modelled | 45.3 | 19 | Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:4HBT-like
27 | c1m1gB_ |
| not modelled | 44.2 | 18 | PDB header:transcription Chain: B: PDB Molecule:transcription antitermination protein nusg; PDBTitle: crystal structure of aquifex aeolicus n-utilization2 substance g (nusg), space group p2(1)
28 | d2coya1 |
| not modelled | 43.8 | 28 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
29 | c4a1cS_ |
| not modelled | 43.0 | 18 | PDB header:ribosome Chain: S: PDB Molecule:rpl26; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4.
30 | d1ylia1 |
| not modelled | 42.3 | 18 | Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:4HBT-like
31 | d1vpma_ |
| not modelled | 41.1 | 32 | Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:4HBT-like
32 | d2cqaa1 |
| not modelled | 38.8 | 28 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:TIP49 domain
33 | c4a2iV_ |
| not modelled | 38.8 | 21 | PDB header:ribosome/hydrolase Chain: V: PDB Molecule:putative ribosome biogenesis gtpase rsga; PDBTitle: cryo-electron microscopy structure of the 30s subunit in complex with2 the yjeq biogenesis factor
34 | d1vqot1 |
| not modelled | 38.5 | 32 | Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:Ribosomal proteins L24p and L21e
35 | c1u0lB_ |
| not modelled | 37.0 | 22 | PDB header:hydrolase Chain: B: PDB Molecule:probable gtpase engc; PDBTitle: crystal structure of yjeq from thermotoga maritima
36 | c2v1oF_ |
| not modelled | 35.1 | 11 | PDB header:hydrolase Chain: F: PDB Molecule:cytosolic acyl coenzyme a thioester hydrolase; PDBTitle: crystal structure of n-terminal domain of acyl-coa2 thioesterase 7
37 | d2cp6a1 |
| not modelled | 35.0 | 29 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
38 | d2do3a1 |
| not modelled | 33.9 | 22 | Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:SPT5 KOW domain-like
39 | d1ppje2 |
| not modelled | 33.7 | 8 | Fold:Single transmembrane helix Superfamily:ISP transmembrane anchor Family:ISP transmembrane anchor
40 | c3iz5Y_ |
| not modelled | 31.8 | 18 | PDB header:ribosome Chain: Y: PDB Molecule:60s ribosomal protein l26 (l24p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
41 | d1yvca1 |
| not modelled | 31.4 | 19 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:TRAM domain
42 | d1yeza1 |
| not modelled | 30.7 | 11 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:TRAM domain
43 | c2qq2C_ |
| not modelled | 30.0 | 11 | PDB header:hydrolase Chain: C: PDB Molecule:cytosolic acyl coenzyme a thioester hydrolase; PDBTitle: crystal structure of c-terminal domain of human acyl-coa thioesterase2 7
44 | d2coza1 |
| not modelled | 29.7 | 17 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
45 | c2xhcA_ |
| not modelled | 29.3 | 22 | PDB header:transcription Chain: A: PDB Molecule:transcription antitermination protein nusg; PDBTitle: crystal structure of thermotoga maritima n-utilization substance g2 (nusg)
46 | d1bcce2 |
| not modelled | 28.6 | 8 | Fold:Single transmembrane helix Superfamily:ISP transmembrane anchor Family:ISP transmembrane anchor
47 | c2z0wA_ |
| not modelled | 27.7 | 24 | PDB header:protein binding Chain: A: PDB Molecule:cap-gly domain-containing linker protein 4; PDBTitle: crystal structure of the 2nd cap-gly domain in human restin-2 like protein 2 reveals a swapped-dimer
48 | c3d6lA_ |
| not modelled | 27.1 | 23 | PDB header:hydrolase Chain: A: PDB Molecule:putative hydrolase; PDBTitle: crystal structure of cj0915, a hexameric hotdog fold2 thioesterase of campylobacter jejuni
49 | d2e3ha1 |
| not modelled | 26.9 | 33 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
50 | d2cp5a1 |
| not modelled | 26.9 | 14 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
51 | d2cp3a1 |
| not modelled | 26.7 | 33 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
52 | c2eisA_ |
| not modelled | 26.5 | 23 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein tthb207; PDBTitle: x-ray structure of acyl-coa hydrolase-like protein, tt1379, from2 thermus thermophilus hb8
53 | d2e3ia1 |
| not modelled | 26.4 | 14 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
54 | d1whja_ |
| not modelled | 25.8 | 32 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
55 | c2e4hA_ |
| not modelled | 24.7 | 30 | PDB header:structural protein Chain: A: PDB Molecule:restin; PDBTitle: solution structure of cytoskeletal protein in complex with2 tubulin tail
56 | d1ayia_ |
| not modelled | 24.6 | 24 | Fold:Acyl carrier protein-like Superfamily:Colicin E immunity proteins Family:Colicin E immunity proteins
57 | d2cowa1 |
| not modelled | 24.2 | 22 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
58 | d2cp2a1 |
| not modelled | 23.8 | 19 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
59 | d2vlqa1 |
| not modelled | 23.4 | 24 | Fold:Acyl carrier protein-like Superfamily:Colicin E immunity proteins Family:Colicin E immunity proteins
60 | c3owvA_ |
| not modelled | 23.3 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:dna-entry nuclease; PDBTitle: structural insights into catalytic and substrate binding mechanisms of2 the strategic enda nuclease from streptococcus pneumoniae
61 | c2no8A_ |
| not modelled | 22.2 | 30 | PDB header:immune system Chain: A: PDB Molecule:colicin-e2 immunity protein; PDBTitle: nmr structure analysis of the colicin immuntiy protein im2
62 | d2cp0a1 |
| not modelled | 22.2 | 22 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
63 | c3mayE_ |
| not modelled | 20.1 | 27 | PDB header:heme-binding protein Chain: E: PDB Molecule:possible exported protein; PDBTitle: crystal structure of a secreted mycobacterium tuberculosis heme-2 binding protein
64 | d1gxha_ |
| not modelled | 19.9 | 30 | Fold:Acyl carrier protein-like Superfamily:Colicin E immunity proteins Family:Colicin E immunity proteins
65 | c3lwgB_ |
| not modelled | 19.4 | 4 | PDB header:unknown function Chain: B: PDB Molecule:hp0420 homologue; PDBTitle: crystal structure of hp0420-homologue c46a from helicobacter2 felis
66 | d1njjb1 |
| not modelled | 18.8 | 33 | Fold:Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily:Alanine racemase C-terminal domain-like Family:Eukaryotic ODC-like
67 | d1whha_ |
| not modelled | 17.4 | 21 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
68 | d2btva_ |
| not modelled | 17.2 | 26 | Fold:Reovirus inner layer core protein p3 Superfamily:Reovirus inner layer core protein p3 Family:Orbivirus core
69 | c2zqeA_ |
| not modelled | 16.4 | 35 | PDB header:dna binding protein Chain: A: PDB Molecule:muts2 protein; PDBTitle: crystal structure of the smr domain of thermus thermophilus muts2
70 | d2cbpa_ |
| not modelled | 16.2 | 25 | Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like
71 | d1i9ga_ |
| not modelled | 15.8 | 8 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:tRNA(1-methyladenosine) methyltransferase-like
72 | d2toda1 |
| not modelled | 15.6 | 33 | Fold:Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily:Alanine racemase C-terminal domain-like Family:Eukaryotic ODC-like
73 | d2je6i1 |
| not modelled | 15.1 | 19 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
74 | c2btvB_ |
| not modelled | 14.7 | 26 | PDB header:virus Chain: B: PDB Molecule:protein (vp3 core protein); PDBTitle: atomic model for bluetongue virus (btv) core
75 | d1y4oa1 |
| not modelled | 14.3 | 19 | Fold:Profilin-like Superfamily:Roadblock/LC7 domain Family:Roadblock/LC7 domain
76 | d2ot2a1 |
| not modelled | 13.7 | 20 | Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like
77 | d1sroa_ |
| not modelled | 13.7 | 12 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
78 | c1s1iU_ |
| not modelled | 13.4 | 18 | PDB header:ribosome Chain: U: PDB Molecule:60s ribosomal protein l26-a; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.
79 | d1bbua1 |
| not modelled | 13.3 | 22 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Anticodon-binding domain
80 | d1ws8a_ |
| not modelled | 12.6 | 21 | Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like
81 | d1e1oa1 |
| not modelled | 12.3 | 19 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Anticodon-binding domain
82 | d1e32a3 |
| not modelled | 12.2 | 21 | Fold:Cdc48 domain 2-like Superfamily:Cdc48 domain 2-like Family:Cdc48 domain 2-like
83 | d2g50a1 |
| not modelled | 12.1 | 14 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
84 | d3d3ra1 |
| not modelled | 12.1 | 25 | Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like
85 | d1r4va_ |
| not modelled | 11.8 | 23 | Fold:Histone-fold Superfamily:Histone-fold Family:Bacterial histone-fold protein
86 | d1g7sa1 |
| not modelled | 11.7 | 26 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors
87 | c2qlwA_ |
| not modelled | 11.6 | 21 | PDB header:isomerase Chain: A: PDB Molecule:rhau; PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum
88 | c2qlxA_ |
| not modelled | 11.6 | 21 | PDB header:isomerase Chain: A: PDB Molecule:l-rhamnose mutarotase; PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum in complex with l-rhamnose
89 | d1wwia1 |
| not modelled | 11.5 | 14 | Fold:Histone-fold Superfamily:Histone-fold Family:Bacterial histone-fold protein
90 | d1ubea2 |
| not modelled | 11.5 | 7 | Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain
91 | c2gutA_ |
| not modelled | 11.5 | 23 | PDB header:transcription Chain: A: PDB Molecule:arc/mediator, positive cofactor 2 glutamine/q- PDBTitle: solution structure of the trans-activation domain of the2 human co-activator arc105
92 | d1mo6a2 |
| not modelled | 11.5 | 7 | Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain
93 | c3d3rA_ |
| not modelled | 11.4 | 25 | PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1
94 | d1d7ka1 |
| not modelled | 11.2 | 33 | Fold:Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily:Alanine racemase C-terminal domain-like Family:Eukaryotic ODC-like
95 | c3g7gG_ |
| not modelled | 11.1 | 18 | PDB header:structural genomics, unknown function Chain: G: PDB Molecule:upf0311 protein ca_c3321; PDBTitle: crystal structure of the protein with unknown function from2 clostridium acetobutylicum atcc 824
96 | d1g7sa2 |
| not modelled | 11.1 | 19 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors
97 | d1e0ta1 |
| not modelled | 11.1 | 21 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
98 | d1jera_ |
| not modelled | 11.0 | 29 | Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like
99 | c1jerA_ |
| not modelled | 11.0 | 29 | PDB header:electron transport Chain: A: PDB Molecule:cucumber stellacyanin; PDBTitle: cucumber stellacyanin, cu2+, ph 7.0

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