Phyre 2 Results for P36661

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Email | l.a.kelley@imperial.ac.uk
Description | P36661
Date | Thu Jan 5 11:53:33 GMT 2012
Unique Job ID | 20c5f8f862434c9d

Summary |

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

Model (left) based on template c3pfyA_
Top template information
PDB header:hydrolase Chain: A: PDB Molecule:otu domain-containing protein 5; PDBTitle: the catalytic domain of human otud5
Confidence and coverage
Confidence: | 93.3% | Coverage: | 6%
27 residues ( 6% of your sequence) have been modelled with 93.3% 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 | G | S | N | I | H | G | I | S | C | T | A | N | N | Y | L | K | Q | A | W | N | D | I | K | N | E | Y | E | K | N | Q | T | Y | S | I | T | L | F | E | N | T | L | V | C | F | M | R | L | Y | N | E | L | R | R | K | V | N | E | E | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | T | P | C | L | E | C | E | S | L | E | K | E | F | E | E | M | Q | N | D | N | D | L | S | L | F | M | R | I | L | R | T | N | D | T | Q | I | Y | S | G | V | S | G | G | I | T | Y | T | I | Q | Y | V | R | D | I | D | I | V | R | V | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | L | P | G | R | A | S | E | S | I | T | D | F | K | G | Y | Y | W | Y | N | F | M | E | Y | I | E | N | I | N | A | C | D | D | V | F | S | E | Y | C | F | D | D | E | N | I | S | V | Q | P | E | R | I | N | T | P | G | I | S | D | L | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  | ? |  |  |  |  | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | S | D | I | D | L | S | G | I | S | F | I | Q | R | E | T | N | Q | A | L | G | L | K | Y | A | P | V | D | G | D | G | Y | C | L | L | R | A | I | L | V | L | K | Q | H | D | Y | S | W | A | L | V | S | Y | K | M | Q | K | E | V | Y | N
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | E | F | I | K | M | V | D | K | K | T | I | E | A | L | V | D | T | A | F | Y | N | L | R | E | D | V | K | T | L | F | G | V | D | L | Q | S | D | N | Q | I | Q | G | Q | S | S | L | M | S | W | S | F | L | F | F | K | K | Q | F | I | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | . | . | . | . | . | 360
Sequence |  | S | C | L | N | N | E | K | C | I | L | H | L | P | E | F | I | F | N | D | N | K | N | L | L | A | L | D | T | D | T | S | D | R | I | K | A | V | K | N | F | L | V | V | L | S | D | S | I | C | S | L | F | I | V | N | S | N | V | A | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 370 | . | . | . | . | . | . | . | . | . | 380 | . | . | . | . | . | . | . | . | . | 390 | . | . | . | . | . | . | . | . | . | 400 | . | . | . | . | . | . | . | . | . | 410 | . | . | . | . | . | . | . | .
Sequence |  | I | S | L | G | N | E | S | F | S | T | D | E | D | L | E | Y | G | Y | L | M | N | T | G | N | H | Y | D | V | Y | L | P | P | E | L | F | A | Q | A | Y | K | L | N | N | K | E | M | N | A | Q | L | D | Y | L | N | R | Y | A | I
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 |
| c3pfyA_ |

### PDB 3pfy chain A

Region: 191 - 217
Aligned: 27
Modelled: 27
Confidence: 93.3%
Identity: 26%
PDB header:hydrolase
Chain: A: PDB Molecule:otu domain-containing protein 5;
PDBTitle: the catalytic domain of human otud5

Phyre2
2 |
| c2zfyA_ |

### PDB 2zfy chain A

Region: 203 - 218
Aligned: 16
Modelled: 16
Confidence: 80.8%
Identity: 31%
PDB header:hydrolase
Chain: A: PDB Molecule:ubiquitin thioesterase otub1;
PDBTitle: crystal structure of human otubain 1

Phyre2
3 |
| c3c0rC_ |

### PDB 3c0r chain C

Region: 201 - 217
Aligned: 17
Modelled: 17
Confidence: 80.5%
Identity: 47%
PDB header:cell cycle, hydrolase
Chain: C: PDB Molecule:ubiquitin thioesterase otu1;
PDBTitle: structure of ovarian tumor (otu) domain in complex with ubiquitin

Phyre2
4 |
| c3pt2A_ |

### PDB 3pt2 chain A

Region: 196 - 217
Aligned: 22
Modelled: 22
Confidence: 72.8%
Identity: 27%
PDB header:hydrolase/protein binding
Chain: A: PDB Molecule:rna polymerase;
PDBTitle: structure of a viral otu domain protease bound to ubiquitin

Phyre2
5 |
| d1tffa_ |

### PDB 1tff chain A

Region: 203 - 218
Aligned: 16
Modelled: 16
Confidence: 69.4%
Identity: 31%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Ubiquitin thiolesterase protein OTUB2 (Otubain-2)

Phyre2
6 |
| d2d32a1 |

### PDB 2d32 chain A domain 1

Region: 315 - 410
Aligned: 85
Modelled: 96
Confidence: 51.7%
Identity: 31%
Fold: Glutamine synthetase/guanido kinase
Superfamily: Glutamine synthetase/guanido kinase
Family: Glutamate-cysteine ligase

Phyre2
7 |
| c3i7fA_ |

### PDB 3i7f chain A

Region: 282 - 352
Aligned: 69
Modelled: 71
Confidence: 41.2%
Identity: 19%
PDB header:ligase
Chain: A: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: aspartyl trna synthetase from entamoeba histolytica

Phyre2
8 |
| c1u9pA_ |

### PDB 1u9p chain A

Region: 383 - 410
Aligned: 28
Modelled: 28
Confidence: 39.3%
Identity: 25%
PDB header:unknown function
Chain: A: PDB Molecule:parc;
PDBTitle: permuted single-chain arc

Phyre2
9 |
| c1asyA_ |

### PDB 1asy chain A

Region: 282 - 352
Aligned: 69
Modelled: 71
Confidence: 36.1%
Identity: 19%
PDB header:complex (aminoacyl-trna synthase/trna)
Chain: A: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: class ii aminoacyl transfer rna synthetases: crystal2 structure of yeast aspartyl-trna synthetase complexed with3 trna asp

Phyre2
10 |
| c3m4qA_ |

### PDB 3m4q chain A

Region: 282 - 352
Aligned: 64
Modelled: 71
Confidence: 35.9%
Identity: 19%
PDB header:ligase
Chain: A: PDB Molecule:asparaginyl-trna synthetase, putative;
PDBTitle: entamoeba histolytica asparaginyl-trna synthetase (asnrs)

Phyre2
11 |
| d1mnta_ |

### PDB 1mnt chain A

Region: 385 - 410
Aligned: 26
Modelled: 26
Confidence: 27.8%
Identity: 27%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: Arc/Mnt-like phage repressors

Phyre2
12 |
| c1b8aB_ |

### PDB 1b8a chain B

Region: 282 - 348
Aligned: 65
Modelled: 67
Confidence: 23.7%
Identity: 15%
PDB header:ligase
Chain: B: PDB Molecule:protein (aspartyl-trna synthetase);
PDBTitle: aspartyl-trna synthetase

Phyre2
13 |
| c3ln7A_ |

### PDB 3ln7 chain A

Region: 376 - 409
Aligned: 34
Modelled: 34
Confidence: 23.4%
Identity: 32%
PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 pasteurella multocida

Phyre2
14 |
| d1ppjw_ |

### PDB 1ppj chain W

Region: 20 - 29
Aligned: 10
Modelled: 10
Confidence: 20.5%
Identity: 60%
Fold: Single transmembrane helix
Superfamily: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2
15 |
| d1ppjj_ |

### PDB 1ppj chain J

Region: 20 - 29
Aligned: 10
Modelled: 10
Confidence: 19.0%
Identity: 60%
Fold: Single transmembrane helix
Superfamily: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2
16 |
| d2outa1 |

### PDB 2out chain A domain 1

Region: 187 - 209
Aligned: 23
Modelled: 23
Confidence: 17.3%
Identity: 43%
Fold: LEM/SAP HeH motif
Superfamily: Rho N-terminal domain-like
Family: YqbF C-terminal domain-like

Phyre2
17 |
| c3ln6A_ |

### PDB 3ln6 chain A

Region: 376 - 405
Aligned: 30
Modelled: 30
Confidence: 16.6%
Identity: 33%
PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 streptococcus agalactiae

Phyre2
18 |
| d2gp4a1 |

### PDB 2gp4 chain A domain 1

Region: 97 - 125
Aligned: 29
Modelled: 28
Confidence: 16.1%
Identity: 38%
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: LeuD/IlvD-like
Family: IlvD/EDD C-terminal domain-like

Phyre2
19 |
| c2vfjA_ |

### PDB 2vfj chain A

Region: 206 - 218
Aligned: 13
Modelled: 13
Confidence: 16.1%
Identity: 46%
PDB header:hydrolase
Chain: A: PDB Molecule:tumor necrosis factor;
PDBTitle: structure of the a20 ovarian tumour (otu) domain

Phyre2
20 |
| d1y1oa_ |

### PDB 1y1o chain A

Region: 113 - 136
Aligned: 24
Modelled: 24
Confidence: 16.0%
Identity: 46%
Fold: Restriction endonuclease-like
Superfamily: Restriction endonuclease-like
Family: RecU-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3pfyA_ |
|  | 93.3 | 26 | PDB header:hydrolase Chain: A: PDB Molecule:otu domain-containing protein 5; PDBTitle: the catalytic domain of human otud5
2 | c2zfyA_ |
|  | 80.8 | 31 | PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin thioesterase otub1; PDBTitle: crystal structure of human otubain 1
3 | c3c0rC_ |
|  | 80.5 | 47 | PDB header:cell cycle, hydrolase Chain: C: PDB Molecule:ubiquitin thioesterase otu1; PDBTitle: structure of ovarian tumor (otu) domain in complex with ubiquitin
4 | c3pt2A_ |
|  | 72.8 | 27 | PDB header:hydrolase/protein binding Chain: A: PDB Molecule:rna polymerase; PDBTitle: structure of a viral otu domain protease bound to ubiquitin
5 | d1tffa_ |
|  | 69.4 | 31 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Ubiquitin thiolesterase protein OTUB2 (Otubain-2)
6 | d2d32a1 |
|  | 51.7 | 31 | Fold:Glutamine synthetase/guanido kinase Superfamily:Glutamine synthetase/guanido kinase Family:Glutamate-cysteine ligase
7 | c3i7fA_ |
|  | 41.2 | 19 | PDB header:ligase Chain: A: PDB Molecule:aspartyl-trna synthetase; PDBTitle: aspartyl trna synthetase from entamoeba histolytica
8 | c1u9pA_ |
|  | 39.3 | 25 | PDB header:unknown function Chain: A: PDB Molecule:parc; PDBTitle: permuted single-chain arc
9 | c1asyA_ |
|  | 36.1 | 19 | PDB header:complex (aminoacyl-trna synthase/trna) Chain: A: PDB Molecule:aspartyl-trna synthetase; PDBTitle: class ii aminoacyl transfer rna synthetases: crystal2 structure of yeast aspartyl-trna synthetase complexed with3 trna asp
10 | c3m4qA_ |
|  | 35.9 | 19 | PDB header:ligase Chain: A: PDB Molecule:asparaginyl-trna synthetase, putative; PDBTitle: entamoeba histolytica asparaginyl-trna synthetase (asnrs)
11 | d1mnta_ |
|  | 27.8 | 27 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors
12 | c1b8aB_ |
|  | 23.7 | 15 | PDB header:ligase Chain: B: PDB Molecule:protein (aspartyl-trna synthetase); PDBTitle: aspartyl-trna synthetase
13 | c3ln7A_ |
|  | 23.4 | 32 | PDB header:ligase Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab; PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 pasteurella multocida
14 | d1ppjw_ |
|  | 20.5 | 60 | Fold:Single transmembrane helix Superfamily:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
15 | d1ppjj_ |
|  | 19.0 | 60 | Fold:Single transmembrane helix Superfamily:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
16 | d2outa1 |
|  | 17.3 | 43 | Fold:LEM/SAP HeH motif Superfamily:Rho N-terminal domain-like Family:YqbF C-terminal domain-like
17 | c3ln6A_ |
|  | 16.6 | 33 | PDB header:ligase Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab; PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 streptococcus agalactiae
18 | d2gp4a1 |
|  | 16.1 | 38 | Fold:The "swivelling" beta/beta/alpha domain Superfamily:LeuD/IlvD-like Family:IlvD/EDD C-terminal domain-like
19 | c2vfjA_ |
|  | 16.1 | 46 | PDB header:hydrolase Chain: A: PDB Molecule:tumor necrosis factor; PDBTitle: structure of the a20 ovarian tumour (otu) domain
20 | d1y1oa_ |
|  | 16.0 | 46 | Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:RecU-like
21 | c1y1oC_ |
| not modelled | 16.0 | 46 | PDB header:recombination Chain: C: PDB Molecule:penicillin-binding protein-related factor a; PDBTitle: x-ray crystal structure of penicillin-binding protein-2 related factor a from bacillus stearothermophilus
22 | c3dkbA_ |
| not modelled | 15.9 | 46 | PDB header:hydrolase Chain: A: PDB Molecule:tumor necrosis factor, alpha-induced protein 3; PDBTitle: crystal structure of a20, 2.5 angstrom
23 | c3c0mB_ |
| not modelled | 13.6 | 28 | PDB header:toxin Chain: B: PDB Molecule:aerolysin; PDBTitle: crystal structure of the proaerolysin mutant y221g
24 | d1thqa_ |
| not modelled | 11.8 | 45 | Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane enzyme PagP
25 | d1sg7a1 |
| not modelled | 11.6 | 47 | Fold:ChaB-like Superfamily:ChaB-like Family:ChaB-like
26 | c1sg7A_ |
| not modelled | 11.6 | 47 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cation transport regulator chab; PDBTitle: nmr solution structure of the putative cation transport2 regulator chab
27 | d1r4xa2 |
| not modelled | 11.6 | 24 | Fold:Subdomain of clathrin and coatomer appendage domain Superfamily:Subdomain of clathrin and coatomer appendage domain Family:Coatomer appendage domain
28 | c2xgtB_ |
| not modelled | 10.9 | 29 | PDB header:ligase Chain: B: PDB Molecule:asparaginyl-trna synthetase, cytoplasmic; PDBTitle: asparaginyl-trna synthetase from brugia malayi complexed2 with the sulphamoyl analogue of asparaginyl-adenylate
29 | c3oakC_ |
| not modelled | 10.8 | 86 | PDB header:transcription Chain: C: PDB Molecule:transcription elongation factor spt6; PDBTitle: crystal structure of a spn1 (iws1)-spt6 complex
30 | d2ftxb1 |
| not modelled | 10.3 | 28 | Fold:Kinetochore globular domain-like Superfamily:Kinetochore globular domain Family:Spc24-like
31 | c2fv4B_ |
| not modelled | 10.2 | 28 | PDB header:structural protein, protein binding Chain: B: PDB Molecule:hypothetical 24.6 kda protein in ilv2-ade17 PDBTitle: nmr solution structure of the yeast kinetochore spc24/spc252 globular domain
32 | c2vxdA_ |
| not modelled | 9.8 | 11 | PDB header:nuclear protein Chain: A: PDB Molecule:nucleophosmin; PDBTitle: the structure of the c-terminal domain of nucleophosmin
33 | c1ykuB_ |
| not modelled | 9.8 | 19 | PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein pxo2-61; PDBTitle: crystal structure of a sensor domain homolog
34 | c2rodB_ |
| not modelled | 9.6 | 53 | PDB header:apoptosis Chain: B: PDB Molecule:noxa; PDBTitle: solution structure of mcl-1 complexed with noxaa
35 | c1e22A_ |
| not modelled | 9.5 | 21 | PDB header:ligase Chain: A: PDB Molecule:lysyl-trna synthetase; PDBTitle: lysyl-trna synthetase (lysu) hexagonal form complexed with2 lysine and the non-hydrolysable atp analogue amp-pcp
36 | d2cura2 |
| not modelled | 9.5 | 100 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
37 | c2yfvC_ |
| not modelled | 9.3 | 33 | PDB header:cell cycle Chain: C: PDB Molecule:scm3; PDBTitle: the heterotrimeric complex of kluyveromyces lactis scm3, cse4 and h4
38 | c1p5kA_ |
| not modelled | 9.3 | 64 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution ser to leu11 modification in sds-d252 micelles
39 | c2jwnB_ |
| not modelled | 8.4 | 34 | PDB header:rna binding protein Chain: B: PDB Molecule:embryonic polyadenylate-binding protein 2-b; PDBTitle: solution nmr structure of the protease-resistent domain of2 xenopus laevis epabp2
40 | c2npiB_ |
| not modelled | 8.2 | 26 | PDB header:transcription Chain: B: PDB Molecule:protein clp1; PDBTitle: clp1-atp-pcf11 complex
41 | c3nztA_ |
| not modelled | 8.1 | 27 | PDB header:ligase Chain: A: PDB Molecule:glutamate--cysteine ligase; PDBTitle: 2.0 angstrom crystal structure of glutamate--cysteine ligase (gsha)2 ftom francisella tularensis in complex with amp
42 | d2d8za1 |
| not modelled | 7.7 | 67 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
43 | c2lc0A_ |
| not modelled | 7.6 | 18 | PDB header:protein binding Chain: A: PDB Molecule:putative uncharacterized protein tb39.8; PDBTitle: rv0020c_nter structure
44 | c3bjuB_ |
| not modelled | 7.6 | 24 | PDB header:ligase Chain: B: PDB Molecule:lysyl-trna synthetase; PDBTitle: crystal structure of tetrameric form of human lysyl-trna2 synthetase
45 | d1o57a1 |
| not modelled | 7.6 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:N-terminal domain of Bacillus PurR
46 | c1sfcD_ |
| not modelled | 7.5 | 20 | PDB header:transport protein Chain: D: PDB Molecule:protein (snap-25b); PDBTitle: neuronal synaptic fusion complex
47 | c2v4oB_ |
| not modelled | 6.9 | 46 | PDB header:hydrolase Chain: B: PDB Molecule:multifunctional protein sur e; PDBTitle: crystal structure of salmonella typhimurium sure at 2.752 angstrom resolution in monoclinic form
48 | d2i9fa1 |
| not modelled | 6.9 | 44 | Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Arterivirus nucleocapsid protein
49 | c2gloA_ |
| not modelled | 6.9 | 32 | PDB header:transcription/dna Chain: A: PDB Molecule:brinker cg9653-pa; PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer
50 | c2yv5A_ |
| not modelled | 6.9 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:yjeq protein; PDBTitle: crystal structure of yjeq from aquifex aeolicus
51 | c3c2vA_ |
| not modelled | 6.7 | 20 | PDB header:transferase Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase; PDBTitle: crystal structure of the quinolinate phosphoribosyl2 transferase (bna6) from saccharomyces cerevisiae complexed3 with prpp and the inhibitor phthalate
52 | c2f0cC_ |
| not modelled | 6.7 | 28 | PDB header:virus/viral protein Chain: C: PDB Molecule:phage tp901-1 orf49 (bpp); PDBTitle: structure of the receptor binding protein (orf49, bbp) from lactophage2 tp901-1
53 | c1wydB_ |
| not modelled | 6.6 | 23 | PDB header:ligase Chain: B: PDB Molecule:hypothetical aspartyl-trna synthetase; PDBTitle: crystal structure of aspartyl-trna synthetase from sulfolobus tokodaii
54 | c1aq5C_ |
| not modelled | 6.4 | 58 | PDB header:coiled-coil Chain: C: PDB Molecule:cartilage matrix protein; PDBTitle: high-resolution solution nmr structure of the trimeric coiled-coil2 domain of chicken cartilage matrix protein, 20 structures
55 | c1x55A_ |
| not modelled | 6.4 | 21 | PDB header:ligase Chain: A: PDB Molecule:asparaginyl-trna synthetase; PDBTitle: crystal structure of asparaginyl-trna synthetase from pyrococcus2 horikoshii complexed with asparaginyl-adenylate analogue
56 | c3e9hB_ |
| not modelled | 6.3 | 18 | PDB header:ligase Chain: B: PDB Molecule:lysyl-trna synthetase; PDBTitle: lysyl-trna synthetase from bacillus stearothermophilus2 complexed with l-lysylsulfamoyl adenosine
57 | d2enga_ |
| not modelled | 6.2 | 38 | Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:Eng V-like
58 | d1eova2 |
| not modelled | 6.1 | 18 | Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
59 | d1f0la3 |
| not modelled | 6.0 | 25 | Fold:Toxins' membrane translocation domains Superfamily:Diphtheria toxin, middle domain Family:Diphtheria toxin, middle domain
60 | d2duca1 |
| not modelled | 5.8 | 26 | Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold
61 | c2i8bB_ |
| not modelled | 5.8 | 30 | PDB header:viral protein Chain: B: PDB Molecule:minor nucleoprotein vp30; PDBTitle: crystal structure of the c-terminal domain of ebola virus vp30
62 | d2al6a2 |
| not modelled | 5.7 | 83 | Fold:PH domain-like barrel Superfamily:PH domain-like Family:Third domain of FERM
63 | d2cs7a1 |
| not modelled | 5.6 | 24 | Fold:IL8-like Superfamily:PhtA domain-like Family:PhtA domain-like
64 | c1p5lA_ |
| not modelled | 5.6 | 64 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution phe5 to ser modification in sds-d252 micelles
65 | c1p0gA_ |
| not modelled | 5.4 | 64 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy
66 | c2e6gI_ |
| not modelled | 5.4 | 31 | PDB header:hydrolase Chain: I: PDB Molecule:5'-nucleotidase sure; PDBTitle: crystal structure of the stationary phase survival protein sure from2 thermus thermophilus hb8 in complex with phosphate
67 | c3pmdA_ |
| not modelled | 5.2 | 24 | PDB header:lipid binding protein Chain: A: PDB Molecule:conserved domain protein; PDBTitle: crystal structure of the sporulation inhibitor pxo1-118 from bacillus2 anthracis
68 | d2saka_ |
| not modelled | 5.1 | 21 | Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase

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