Phyre 2 Results for P69805

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Email | l.a.kelley@imperial.ac.uk
Description | P69805
Date | Thu Jan 5 12:12:01 GMT 2012
Unique Job ID | faecc54ca0d9980c

Summary |

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

Model (left) based on template c2dmwA_
Top template information
PDB header:membrane protein Chain: A: PDB Molecule:synaptobrevin-like 1 variant; PDBTitle: solution structure of the longin domain of synaptobrevin-2 like protein 1
Confidence and coverage
Confidence: | 37.4% | Coverage: | 16%
45 residues ( 16% of your sequence) have been modelled with 37.4% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | V | D | T | T | Q | T | T | T | E | K | K | L | T | Q | S | D | I | R | G | V | F | L | R | S | N | L | F | Q | G | S | W | N | F | E | R | M | Q | A | L | G | F | C | F | S | M | V | P | A | I | R | R | L | Y | P | E | N | N | E | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | R | K | Q | A | I | R | R | H | L | E | F | F | N | T | Q | P | F | V | A | A | P | I | L | G | V | T | L | A | L | E | E | Q | R | A | N | G | A | E | I | D | D | G | A | I | N | G | I | K | V | G | L | M | G | P | L | A | G | V | G | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | P | I | F | W | G | T | V | R | P | V | F | A | A | L | G | A | G | I | A | M | S | G | S | L | L | G | P | L | L | F | F | I | L | F | N | L | V | R | L | A | T | R | Y | Y | G | V | A | Y | G | Y | S | K | G | I | D | I | V | K | D | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | G | G | G | F | L | Q | K | L | T | E | G | A | S | I | L | G | L | F | V | M | G | A | L | V | N | K | W | T | H | V | N | I | P | L | V | V | S | R | I | T | D | Q | T | G | K | E | H | V | T | T | V | Q | T | I | L | D | Q | L | M | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | .
Sequence |  | G | L | V | P | L | L | L | T | F | A | C | M | W | L | L | R | K | K | V | N | P | L | W | I | I | V | G | F | F | V | I | G | I | A | G | Y | A | C | G | L | L | G | L
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 |
| c2dmwA_ |

### PDB 2dmw chain A

Region: 33 - 77
Aligned: 45
Modelled: 45
Confidence: 37.4%
Identity: 20%
PDB header:membrane protein
Chain: A: PDB Molecule:synaptobrevin-like 1 variant;
PDBTitle: solution structure of the longin domain of synaptobrevin-2 like protein 1

Phyre2
2 |
| c3aqpB_ |

### PDB 3aqp chain B

Region: 238 - 274
Aligned: 37
Modelled: 37
Confidence: 23.9%
Identity: 11%
PDB header:membrane protein
Chain: B: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus

Phyre2
3 |
| d1ljra1 |

### PDB 1ljr chain A domain 1

Region: 51 - 118
Aligned: 64
Modelled: 68
Confidence: 21.6%
Identity: 13%
Fold: GST C-terminal domain-like
Superfamily: GST C-terminal domain-like
Family: Glutathione S-transferase (GST), C-terminal domain

Phyre2
4 |
| d1iyxa2 |

### PDB 1iyx chain A domain 2

Region: 46 - 100
Aligned: 55
Modelled: 55
Confidence: 19.2%
Identity: 24%
Fold: Enolase N-terminal domain-like
Superfamily: Enolase N-terminal domain-like
Family: Enolase N-terminal domain-like

Phyre2
5 |
| c2jttD_ |

### PDB 2jtt chain D

Region: 45 - 67
Aligned: 23
Modelled: 23
Confidence: 17.2%
Identity: 13%
PDB header:calcium binding protein/antitumor protei
Chain: D: PDB Molecule:calcyclin-binding protein;
PDBTitle: solution structure of calcium loaded s100a6 bound to c-2 terminal siah-1 interacting protein

Phyre2
6 |
| c1zroB_ |

### PDB 1zro chain B

Region: 58 - 123
Aligned: 66
Modelled: 66
Confidence: 16.6%
Identity: 12%
PDB header:cell invasion
Chain: B: PDB Molecule:erythrocyte binding antigen region ii;
PDBTitle: crystal structure of eba-175 region ii (rii) crystallized2 in the presence of (alpha)2,3-sialyllactose

Phyre2
7 |
| c3htkB_ |

### PDB 3htk chain B

Region: 43 - 82
Aligned: 39
Modelled: 40
Confidence: 15.8%
Identity: 13%
PDB header:recombination/replication/ligase
Chain: B: PDB Molecule:structural maintenance of chromosomes protein 5;
PDBTitle: crystal structure of mms21 and smc5 complex

Phyre2
8 |
| d1v97a1 |

### PDB 1v97 chain A domain 1

Region: 8 - 69
Aligned: 55
Modelled: 62
Confidence: 14.8%
Identity: 20%
Fold: CO dehydrogenase ISP C-domain like
Superfamily: CO dehydrogenase ISP C-domain like
Family: CO dehydrogenase ISP C-domain like

Phyre2
9 |
| d1oaia_ |

### PDB 1oai chain A

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 13.9%
Identity: 16%
Fold: RuvA C-terminal domain-like
Superfamily: UBA-like
Family: TAP-C domain-like

Phyre2
10 |
| d1axda1 |

### PDB 1axd chain A domain 1

Region: 53 - 111
Aligned: 58
Modelled: 59
Confidence: 13.2%
Identity: 16%
Fold: GST C-terminal domain-like
Superfamily: GST C-terminal domain-like
Family: Glutathione S-transferase (GST), C-terminal domain

Phyre2
11 |
| d1hh4e_ |

### PDB 1hh4 chain E

Region: 88 - 120
Aligned: 31
Modelled: 33
Confidence: 13.1%
Identity: 26%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: E set domains
Family: RhoGDI-like

Phyre2
12 |
| c1yx5A_ |

### PDB 1yx5 chain A

Region: 72 - 95
Aligned: 24
Modelled: 24
Confidence: 12.6%
Identity: 29%
PDB header:hydrolase
Chain: A: PDB Molecule:26s proteasome non-atpase regulatory subunit 4;
PDBTitle: solution structure of s5a uim-1/ubiquitin complex

Phyre2
13 |
| c1yhuW_ |

### PDB 1yhu chain W

Region: 36 - 116
Aligned: 76
Modelled: 81
Confidence: 11.2%
Identity: 8%
PDB header:oxygen storage/transport
Chain: W: PDB Molecule:hemoglobin b1a chain;
PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits.

Phyre2
14 |
| d2i4ra1 |

### PDB 2i4r chain A domain 1

Region: 100 - 122
Aligned: 17
Modelled: 23
Confidence: 10.9%
Identity: 35%
Fold: AtpF-like
Superfamily: AtpF-like
Family: AtpF-like

Phyre2
15 |
| d1ds6b_ |

### PDB 1ds6 chain B

Region: 88 - 120
Aligned: 31
Modelled: 33
Confidence: 10.9%
Identity: 29%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: E set domains
Family: RhoGDI-like

Phyre2
16 |
| c3bd0D_ |

### PDB 3bd0 chain D

Region: 52 - 70
Aligned: 19
Modelled: 19
Confidence: 10.8%
Identity: 11%
PDB header:peptide binding protein
Chain: D: PDB Molecule:protein memo1;
PDBTitle: crystal structure of memo, form ii

Phyre2
17 |
| d3cx5d2 |

### PDB 3cx5 chain D domain 2

Region: 246 - 263
Aligned: 18
Modelled: 18
Confidence: 10.3%
Identity: 17%
Fold: Single transmembrane helix
Superfamily: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
Family: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor

Phyre2
18 |
| d1ppjd2 |

### PDB 1ppj chain D domain 2

Region: 246 - 263
Aligned: 18
Modelled: 18
Confidence: 10.2%
Identity: 28%
Fold: Single transmembrane helix
Superfamily: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
Family: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor

Phyre2
19 |
| c2j96B_ |

### PDB 2j96 chain B

Region: 54 - 72
Aligned: 18
Modelled: 19
Confidence: 10.0%
Identity: 22%
PDB header:photosynthesis
Chain: B: PDB Molecule:phycoerythrocyanin alpha chain;
PDBTitle: the e-configuration of alfa-phycoerythrocyanin

Phyre2
20 |
| c3c9pA_ |

### PDB 3c9p chain A

Region: 49 - 108
Aligned: 55
Modelled: 55
Confidence: 9.9%
Identity: 24%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein sp1917;
PDBTitle: crystal structure of uncharacterized protein sp1917

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2dmwA_ |
|  | 37.4 | 20 | PDB header:membrane protein Chain: A: PDB Molecule:synaptobrevin-like 1 variant; PDBTitle: solution structure of the longin domain of synaptobrevin-2 like protein 1
2 | c3aqpB_ |
|  | 23.9 | 11 | PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus
3 | d1ljra1 |
|  | 21.6 | 13 | Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain
4 | d1iyxa2 |
|  | 19.2 | 24 | Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like
5 | c2jttD_ |
|  | 17.2 | 13 | PDB header:calcium binding protein/antitumor protei Chain: D: PDB Molecule:calcyclin-binding protein; PDBTitle: solution structure of calcium loaded s100a6 bound to c-2 terminal siah-1 interacting protein
6 | c1zroB_ |
|  | 16.6 | 12 | PDB header:cell invasion Chain: B: PDB Molecule:erythrocyte binding antigen region ii; PDBTitle: crystal structure of eba-175 region ii (rii) crystallized2 in the presence of (alpha)2,3-sialyllactose
7 | c3htkB_ |
|  | 15.8 | 13 | PDB header:recombination/replication/ligase Chain: B: PDB Molecule:structural maintenance of chromosomes protein 5; PDBTitle: crystal structure of mms21 and smc5 complex
8 | d1v97a1 |
|  | 14.8 | 20 | Fold:CO dehydrogenase ISP C-domain like Superfamily:CO dehydrogenase ISP C-domain like Family:CO dehydrogenase ISP C-domain like
9 | d1oaia_ |
|  | 13.9 | 16 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:TAP-C domain-like
10 | d1axda1 |
|  | 13.2 | 16 | Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain
11 | d1hh4e_ |
|  | 13.1 | 26 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like
12 | c1yx5A_ |
|  | 12.6 | 29 | PDB header:hydrolase Chain: A: PDB Molecule:26s proteasome non-atpase regulatory subunit 4; PDBTitle: solution structure of s5a uim-1/ubiquitin complex
13 | c1yhuW_ |
|  | 11.2 | 8 | PDB header:oxygen storage/transport Chain: W: PDB Molecule:hemoglobin b1a chain; PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits.
14 | d2i4ra1 |
|  | 10.9 | 35 | Fold:AtpF-like Superfamily:AtpF-like Family:AtpF-like
15 | d1ds6b_ |
|  | 10.9 | 29 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like
16 | c3bd0D_ |
|  | 10.8 | 11 | PDB header:peptide binding protein Chain: D: PDB Molecule:protein memo1; PDBTitle: crystal structure of memo, form ii
17 | d3cx5d2 |
|  | 10.3 | 17 | Fold:Single transmembrane helix Superfamily:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
18 | d1ppjd2 |
|  | 10.2 | 28 | Fold:Single transmembrane helix Superfamily:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
19 | c2j96B_ |
|  | 10.0 | 22 | PDB header:photosynthesis Chain: B: PDB Molecule:phycoerythrocyanin alpha chain; PDBTitle: the e-configuration of alfa-phycoerythrocyanin
20 | c3c9pA_ |
|  | 9.9 | 24 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917
21 | c1l2aD_ |
| not modelled | 9.7 | 16 | PDB header:hydrolase Chain: D: PDB Molecule:cellobiohydrolase; PDBTitle: the crystal structure and catalytic mechanism of2 cellobiohydrolase cels, the major enzymatic component of3 the clostridium thermocellum cellulosome
22 | d1l1ya_ |
| not modelled | 9.7 | 16 | Fold:alpha/alpha toroid Superfamily:Six-hairpin glycosidases Family:Cellulases catalytic domain
23 | d1go5a_ |
| not modelled | 9.7 | 20 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:TAP-C domain-like
24 | d1vmja_ |
| not modelled | 9.4 | 23 | Fold:YjbQ-like Superfamily:YjbQ-like Family:YjbQ-like
25 | d1k3ra2 |
| not modelled | 9.3 | 19 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:Hypothetical protein MTH1 (MT0001), dimerisation domain
26 | c2kdtA_ |
| not modelled | 9.3 | 50 | PDB header:protein transport Chain: A: PDB Molecule:neuroendocrine convertase 1; PDBTitle: pc1/3 dcsg sorting domain structure in dpc
27 | d1t3qa1 |
| not modelled | 9.1 | 11 | Fold:CO dehydrogenase ISP C-domain like Superfamily:CO dehydrogenase ISP C-domain like Family:CO dehydrogenase ISP C-domain like
28 | d2ebfx1 |
| not modelled | 8.9 | 18 | Fold:PMT central region-like Superfamily:PMT central region-like Family:PMT central region-like
29 | d1xeqa1 |
| not modelled | 8.7 | 50 | Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:N-terminal, RNA-binding domain of nonstructural protein NS1
30 | c2vh3B_ |
| not modelled | 8.6 | 29 | PDB header:unknown function Chain: B: PDB Molecule:ranasmurfin; PDBTitle: ranasmurfin
31 | c3r66A_ |
| not modelled | 8.5 | 50 | PDB header:viral protein/antiviral protein Chain: A: PDB Molecule:non-structural protein 1; PDBTitle: crystal structure of human isg15 in complex with ns1 n-terminal region2 from influenza virus b, northeast structural genomics consortium3 target ids hx6481, hr2873, and or2
32 | d1t33a1 |
| not modelled | 8.3 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
33 | c3cloC_ |
| not modelled | 8.3 | 14 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution
34 | c2qr4B_ |
| not modelled | 8.2 | 8 | PDB header:hydrolase Chain: B: PDB Molecule:peptidase m3b, oligoendopeptidase f; PDBTitle: crystal structure of oligoendopeptidase-f from enterococcus faecium
35 | c2jp7A_ |
| not modelled | 8.2 | 21 | PDB header:translation Chain: A: PDB Molecule:mrna export factor mex67; PDBTitle: nmr structure of the mex67 uba domain
36 | d1f1sa1 |
| not modelled | 8.1 | 21 | Fold:alpha/alpha toroid Superfamily:Chondroitin AC/alginate lyase Family:Hyaluronate lyase-like catalytic, N-terminal domain
37 | d1s29a_ |
| not modelled | 8.1 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:La domain
38 | d1doab_ |
| not modelled | 8.0 | 26 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like
39 | d1r2za1 |
| not modelled | 7.9 | 36 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
40 | d1q33a_ |
| not modelled | 7.9 | 12 | Fold:Nudix Superfamily:Nudix Family:MutT-like
41 | c1bm4A_ |
| not modelled | 7.8 | 38 | PDB header:viral protein Chain: A: PDB Molecule:protein (moloney murine leukemia virus capsid); PDBTitle: momlv capsid protein major homology region peptide analog
42 | d1vi0a2 |
| not modelled | 7.6 | 15 | Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain
43 | d1u7ka_ |
| not modelled | 7.4 | 20 | Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain
44 | d1ee8a1 |
| not modelled | 7.4 | 43 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
45 | d1j2za_ |
| not modelled | 7.3 | 19 | Fold:Single-stranded left-handed beta-helix Superfamily:Trimeric LpxA-like enzymes Family:UDP N-acetylglucosamine acyltransferase
46 | d1g9ga_ |
| not modelled | 7.2 | 16 | Fold:alpha/alpha toroid Superfamily:Six-hairpin glycosidases Family:Cellulases catalytic domain
47 | c2rrfA_ |
| not modelled | 7.2 | 35 | PDB header:unknown function Chain: A: PDB Molecule:zinc finger fyve domain-containing protein 21; PDBTitle: the solution structure of the c-terminal region of zinc finger fyve2 domain-containing protein 21
48 | c1wyoA_ |
| not modelled | 7.1 | 17 | PDB header:structural protein Chain: A: PDB Molecule:microtubule-associated protein rp/eb family PDBTitle: solution structure of the ch domain of human microtubule-2 associated protein rp/eb family member 3
49 | d1utga_ |
| not modelled | 7.1 | 18 | Fold:Uteroglobin-like Superfamily:Uteroglobin-like Family:Uteroglobin-like
50 | d1rm6c1 |
| not modelled | 7.0 | 15 | Fold:CO dehydrogenase ISP C-domain like Superfamily:CO dehydrogenase ISP C-domain like Family:CO dehydrogenase ISP C-domain like
51 | d2cqka1 |
| not modelled | 7.0 | 33 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:La domain
52 | c2r8uA_ |
| not modelled | 6.9 | 20 | PDB header:cell cycle Chain: A: PDB Molecule:microtubule-associated protein rp/eb family PDBTitle: structure of fragment of human end-binding protein 1 (eb1)2 containing the n-terminal domain at 1.35 a resolution
53 | c2p6cB_ |
| not modelled | 6.8 | 19 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:aq_2013 protein; PDBTitle: crystal structure of hypothetical protein aq_2013 from aquifex2 aeolicus vf5.
54 | d1i3da_ |
| not modelled | 6.6 | 14 | Fold:Globin-like Superfamily:Globin-like Family:Globins
55 | d1cb8a1 |
| not modelled | 6.5 | 12 | Fold:alpha/alpha toroid Superfamily:Chondroitin AC/alginate lyase Family:Hyaluronate lyase-like catalytic, N-terminal domain
56 | c2veqA_ |
| not modelled | 6.4 | 40 | PDB header:cell cycle Chain: A: PDB Molecule:centromere dna-binding protein complex cbf3 PDBTitle: insights into kinetochore-dna interactions from the2 structure of cep3p
57 | c1x1jA_ |
| not modelled | 6.3 | 23 | PDB header:lyase Chain: A: PDB Molecule:xanthan lyase; PDBTitle: crystal structure of xanthan lyase (n194a) with a substrate.
58 | d1w6ta2 |
| not modelled | 6.1 | 24 | Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like
59 | c3n8bB_ |
| not modelled | 6.0 | 13 | PDB header:nucleic acid binding protein Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha
60 | c1rm6F_ |
| not modelled | 6.0 | 16 | PDB header:oxidoreductase Chain: F: PDB Molecule:4-hydroxybenzoyl-coa reductase gamma subunit; PDBTitle: structure of 4-hydroxybenzoyl-coa reductase from thauera2 aromatica
61 | d1l2la_ |
| not modelled | 5.9 | 36 | Fold:Ribokinase-like Superfamily:Ribokinase-like Family:ADP-specific Phosphofructokinase/Glucokinase
62 | d1jroa1 |
| not modelled | 5.9 | 16 | Fold:CO dehydrogenase ISP C-domain like Superfamily:CO dehydrogenase ISP C-domain like Family:CO dehydrogenase ISP C-domain like
63 | d2h8aa1 |
| not modelled | 5.8 | 15 | Fold:MAPEG domain-like Superfamily:MAPEG domain-like Family:MAPEG domain
64 | c3zvrA_ |
| not modelled | 5.8 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:dynamin-1; PDBTitle: crystal structure of dynamin
65 | d1m22a_ |
| not modelled | 5.8 | 25 | Fold:Amidase signature (AS) enzymes Superfamily:Amidase signature (AS) enzymes Family:Amidase signature (AS) enzymes
66 | d1alla_ |
| not modelled | 5.7 | 18 | Fold:Globin-like Superfamily:Globin-like Family:Phycocyanin-like phycobilisome proteins
67 | d1tw9a1 |
| not modelled | 5.7 | 12 | Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain
68 | c1cb8A_ |
| not modelled | 5.6 | 5 | PDB header:lyase Chain: A: PDB Molecule:protein (chondroitinase ac); PDBTitle: chondroitinase ac lyase from flavobacterium heparinum
69 | c3nm7D_ |
| not modelled | 5.6 | 13 | PDB header:nucleic acid binding protein Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha
70 | c2rddB_ |
| not modelled | 5.5 | 11 | PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.
71 | c1q0wA_ |
| not modelled | 5.5 | 40 | PDB header:transport protein Chain: A: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: solution structure of vps27 amino-terminal uim-ubiquitin2 complex
72 | d1n9wa2 |
| not modelled | 5.4 | 21 | Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
73 | d1ccda_ |
| not modelled | 5.4 | 15 | Fold:Uteroglobin-like Superfamily:Uteroglobin-like Family:Uteroglobin-like
74 | c3snhA_ |
| not modelled | 5.3 | 17 | PDB header:endocytosis Chain: A: PDB Molecule:dynamin-1; PDBTitle: crystal structure of nucleotide-free human dynamin1
75 | c1k3rA_ |
| not modelled | 5.3 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein mt0001; PDBTitle: crystal structure of the methyltransferase with a knot from2 methanobacterium thermoautotrophicum
76 | d1ffva1 |
| not modelled | 5.2 | 9 | Fold:CO dehydrogenase ISP C-domain like Superfamily:CO dehydrogenase ISP C-domain like Family:CO dehydrogenase ISP C-domain like
77 | d1k1xa1 |
| not modelled | 5.1 | 26 | Fold:immunoglobulin/albumin-binding domain-like Superfamily:Families 57/38 glycoside transferase middle domain Family:4-alpha-glucanotransferase, domain 2
78 | c3b9yA_ |
| not modelled | 5.1 | 10 | PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein

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