Phyre 2 Results for P0AFK0

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Email | l.a.kelley@imperial.ac.uk
Description | P0AFK0
Date | Thu Jan 5 11:26:33 GMT 2012
Unique Job ID | 74ac3b25541de69b

Summary |

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

Model (left) based on template c3qtdC_
Top template information
PDB header:gene regulation Chain: C: PDB Molecule:pmba protein; PDBTitle: crystal structure of putative modulator of gyrase (pmba) from2 pseudomonas aeruginosa pao1
Confidence and coverage
Confidence: | 100.0% | Coverage: | 98%
439 residues ( 98% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | A | L | A | M | K | V | I | S | Q | V | E | A | Q | R | K | I | L | E | E | A | V | S | T | A | L | E | L | A | S | G | K | S | D | G | A | E | V | A | V | S | K | T | T | G | I | S | V | S | T | R | Y | G | E | V | E | N | V | E | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | N | S | D | G | A | L | G | I | T | V | Y | H | Q | N | R | K | G | S | A | S | S | T | D | L | S | P | Q | A | I | A | R | T | V | Q | A | A | L | D | I | A | R | Y | T | S | P | D | P | C | A | G | V | A | D | K | E | L | L | A | F | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  | ? |  | ? | ? |  |  |  |  |  |  | ? | ? | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | A | P | D | L | D | L | F | H | P | A | E | V | S | P | D | E | A | I | E | L | A | A | R | A | E | Q | A | A | L | Q | A | D | K | R | I | T | N | T | E | G | G | S | F | N | S | H | Y | G | V | K | V | F | G | N | S | H | G | M | L | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | G | Y | C | S | T | R | H | S | L | S | S | C | V | I | A | E | E | N | G | D | M | E | R | D | Y | A | Y | T | I | G | R | A | M | S | D | L | Q | T | P | E | W | V | G | A | D | C | A | R | R | T | L | S | R | L | S | P | R | K | L | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | T | M | K | A | P | V | I | F | A | N | E | V | A | T | G | L | F | G | H | L | V | G | A | I | A | G | G | S | V | Y | R | K | S | T | F | L | L | D | S | L | G | K | Q | I | L | P | D | W | L | T | I | E | E | H | P | H | L | L | K | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | . | . | . | . | . | 360
Sequence |  | L | A | S | T | P | F | D | S | E | G | V | R | T | E | R | R | D | I | I | K | D | G | I | L | T | Q | W | L | L | T | S | Y | S | A | R | K | L | G | L | K | S | T | G | H | A | G | G | I | H | N | W | R | I | A | G | Q | G | L | S | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 370 | . | . | . | . | . | . | . | . | . | 380 | . | . | . | . | . | . | . | . | . | 390 | . | . | . | . | . | . | . | . | . | 400 | . | . | . | . | . | . | . | . | . | 410 | . | . | . | . | . | . | . | . | . | 420
Sequence |  | E | Q | M | L | K | E | M | G | T | G | L | V | V | T | E | L | M | G | Q | G | V | S | A | I | T | G | D | Y | S | R | G | A | A | G | F | W | V | E | N | G | E | I | Q | Y | P | V | S | E | I | T | I | A | G | N | L | K | D | M | W | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 430 | . | . | . | . | . | . | . | . | . | 440 | . | . | . | . | . | . | . | . | . | 450
Sequence |  | N | I | V | T | V | G | N | D | I | E | T | R | S | N | I | Q | C | G | S | V | L | L | P | E | M | K | I | A | G | 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 |
| c3qtdC_ |

### PDB 3qtd chain C

Region: 9 - 450
Aligned: 439
Modelled: 442
Confidence: 100.0%
Identity: 50%
PDB header:gene regulation
Chain: C: PDB Molecule:pmba protein;
PDBTitle: crystal structure of putative modulator of gyrase (pmba) from2 pseudomonas aeruginosa pao1

Phyre2
2 |
| d1vpba_ |

### PDB 1vpb chain A

Region: 12 - 449
Aligned: 429
Modelled: 435
Confidence: 100.0%
Identity: 28%
Fold: Putative modulator of DNA gyrase, PmbA/TldD
Superfamily: Putative modulator of DNA gyrase, PmbA/TldD
Family: Putative modulator of DNA gyrase, PmbA/TldD

Phyre2
3 |
| d1vl4a_ |

### PDB 1vl4 chain A

Region: 18 - 448
Aligned: 421
Modelled: 426
Confidence: 100.0%
Identity: 28%
Fold: Putative modulator of DNA gyrase, PmbA/TldD
Superfamily: Putative modulator of DNA gyrase, PmbA/TldD
Family: Putative modulator of DNA gyrase, PmbA/TldD

Phyre2
4 |
| c3onrI_ |

### PDB 3onr chain I

Region: 18 - 69
Aligned: 50
Modelled: 52
Confidence: 25.1%
Identity: 12%
PDB header:metal binding protein
Chain: I: PDB Molecule:protein transport protein sece2;
PDBTitle: crystal structure of the calcium chelating immunodominant antigen,2 calcium dodecin (rv0379),from mycobacterium tuberculosis with a novel3 calcium-binding site

Phyre2
5 |
| d1o12a1 |

### PDB 1o12 chain A domain 1

Region: 381 - 404
Aligned: 21
Modelled: 24
Confidence: 24.5%
Identity: 29%
Fold: Composite domain of metallo-dependent hydrolases
Superfamily: Composite domain of metallo-dependent hydrolases
Family: N-acetylglucosamine-6-phosphate deacetylase, NagA

Phyre2
6 |
| d2ux9a1 |

### PDB 2ux9 chain A domain 1

Region: 18 - 68
Aligned: 49
Modelled: 51
Confidence: 23.2%
Identity: 16%
Fold: Dodecin subunit-like
Superfamily: Dodecin-like
Family: Dodecin-like

Phyre2
7 |
| c2vxaL_ |

### PDB 2vxa chain L

Region: 18 - 68
Aligned: 49
Modelled: 51
Confidence: 23.0%
Identity: 16%
PDB header:flavoprotein
Chain: L: PDB Molecule:dodecin;
PDBTitle: h.halophila dodecin in complex with riboflavin

Phyre2
8 |
| c3oqtP_ |

### PDB 3oqt chain P

Region: 18 - 68
Aligned: 49
Modelled: 51
Confidence: 22.6%
Identity: 14%
PDB header:flavoprotein
Chain: P: PDB Molecule:rv1498a protein;
PDBTitle: crystal structure of rv1498a protein from mycobacterium tuberculosis

Phyre2
9 |
| c3gknA_ |

### PDB 3gkn chain A

Region: 395 - 427
Aligned: 33
Modelled: 33
Confidence: 11.9%
Identity: 12%
PDB header:oxidoreductase
Chain: A: PDB Molecule:bacterioferritin comigratory protein;
PDBTitle: insights into the alkyl peroxide reduction activity of xanthomonas2 campestris bacterioferritin comigratory protein from the trapped3 intermediate/ligand complex structures

Phyre2
10 |
| d1xaca_ |

### PDB 1xac chain A

Region: 210 - 266
Aligned: 50
Modelled: 57
Confidence: 11.5%
Identity: 18%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Dimeric isocitrate & isopropylmalate dehydrogenases

Phyre2
11 |
| d2pjua1 |

### PDB 2pju chain A domain 1

Region: 75 - 103
Aligned: 29
Modelled: 29
Confidence: 9.2%
Identity: 21%
Fold: Chelatase-like
Superfamily: PrpR receptor domain-like
Family: PrpR receptor domain-like

Phyre2
12 |
| c2d1cB_ |

### PDB 2d1c chain B

Region: 210 - 266
Aligned: 50
Modelled: 57
Confidence: 8.9%
Identity: 16%
PDB header:oxidoreductase
Chain: B: PDB Molecule:isocitrate dehydrogenase;
PDBTitle: crystal structure of tt0538 protein from thermus thermophilus hb8

Phyre2
13 |
| d1pb1a_ |

### PDB 1pb1 chain A

Region: 241 - 266
Aligned: 26
Modelled: 26
Confidence: 8.0%
Identity: 15%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Dimeric isocitrate & isopropylmalate dehydrogenases

Phyre2
14 |
| c3ixrA_ |

### PDB 3ixr chain A

Region: 395 - 427
Aligned: 33
Modelled: 33
Confidence: 7.6%
Identity: 9%
PDB header:oxidoreductase
Chain: A: PDB Molecule:bacterioferritin comigratory protein;
PDBTitle: crystal structure of xylella fastidiosa prxq c47s mutant

Phyre2
15 |
| c2iv0A_ |

### PDB 2iv0 chain A

Region: 241 - 266
Aligned: 26
Modelled: 26
Confidence: 7.2%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:isocitrate dehydrogenase;
PDBTitle: thermal stability of isocitrate dehydrogenase from2 archaeoglobus fulgidus studied by crystal structure3 analysis and engineering of chimers

Phyre2
16 |
| d1w0da_ |

### PDB 1w0d chain A

Region: 241 - 266
Aligned: 26
Modelled: 26
Confidence: 6.8%
Identity: 19%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Dimeric isocitrate & isopropylmalate dehydrogenases

Phyre2
17 |
| d1hqsa_ |

### PDB 1hqs chain A

Region: 241 - 266
Aligned: 26
Modelled: 26
Confidence: 6.7%
Identity: 12%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Dimeric isocitrate & isopropylmalate dehydrogenases

Phyre2
18 |
| d1jjga_ |

### PDB 1jjg chain A

Region: 310 - 330
Aligned: 21
Modelled: 21
Confidence: 6.7%
Identity: 38%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2
19 |
| d1n8ja_ |

### PDB 1n8j chain A

Region: 395 - 438
Aligned: 43
Modelled: 44
Confidence: 6.4%
Identity: 23%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Glutathione peroxidase-like

Phyre2
20 |
| c3blxM_ |

### PDB 3blx chain M

Region: 241 - 266
Aligned: 26
Modelled: 26
Confidence: 6.4%
Identity: 15%
PDB header:oxidoreductase
Chain: M: PDB Molecule:isocitrate dehydrogenase [nad] subunit 1;
PDBTitle: yeast isocitrate dehydrogenase (apo form)

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3qtdC_ |
|  | 100.0 | 50 | PDB header:gene regulation Chain: C: PDB Molecule:pmba protein; PDBTitle: crystal structure of putative modulator of gyrase (pmba) from2 pseudomonas aeruginosa pao1
2 | d1vpba_ |
|  | 100.0 | 28 | Fold:Putative modulator of DNA gyrase, PmbA/TldD Superfamily:Putative modulator of DNA gyrase, PmbA/TldD Family:Putative modulator of DNA gyrase, PmbA/TldD
3 | d1vl4a_ |
|  | 100.0 | 28 | Fold:Putative modulator of DNA gyrase, PmbA/TldD Superfamily:Putative modulator of DNA gyrase, PmbA/TldD Family:Putative modulator of DNA gyrase, PmbA/TldD
4 | c3onrI_ |
|  | 25.1 | 12 | PDB header:metal binding protein Chain: I: PDB Molecule:protein transport protein sece2; PDBTitle: crystal structure of the calcium chelating immunodominant antigen,2 calcium dodecin (rv0379),from mycobacterium tuberculosis with a novel3 calcium-binding site
5 | d1o12a1 |
|  | 24.5 | 29 | Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:N-acetylglucosamine-6-phosphate deacetylase, NagA
6 | d2ux9a1 |
|  | 23.2 | 16 | Fold:Dodecin subunit-like Superfamily:Dodecin-like Family:Dodecin-like
7 | c2vxaL_ |
|  | 23.0 | 16 | PDB header:flavoprotein Chain: L: PDB Molecule:dodecin; PDBTitle: h.halophila dodecin in complex with riboflavin
8 | c3oqtP_ |
|  | 22.6 | 14 | PDB header:flavoprotein Chain: P: PDB Molecule:rv1498a protein; PDBTitle: crystal structure of rv1498a protein from mycobacterium tuberculosis
9 | c3gknA_ |
|  | 11.9 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:bacterioferritin comigratory protein; PDBTitle: insights into the alkyl peroxide reduction activity of xanthomonas2 campestris bacterioferritin comigratory protein from the trapped3 intermediate/ligand complex structures
10 | d1xaca_ |
|  | 11.5 | 18 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
11 | d2pjua1 |
|  | 9.2 | 21 | Fold:Chelatase-like Superfamily:PrpR receptor domain-like Family:PrpR receptor domain-like
12 | c2d1cB_ |
|  | 8.9 | 16 | PDB header:oxidoreductase Chain: B: PDB Molecule:isocitrate dehydrogenase; PDBTitle: crystal structure of tt0538 protein from thermus thermophilus hb8
13 | d1pb1a_ |
|  | 8.0 | 15 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
14 | c3ixrA_ |
|  | 7.6 | 9 | PDB header:oxidoreductase Chain: A: PDB Molecule:bacterioferritin comigratory protein; PDBTitle: crystal structure of xylella fastidiosa prxq c47s mutant
15 | c2iv0A_ |
|  | 7.2 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:isocitrate dehydrogenase; PDBTitle: thermal stability of isocitrate dehydrogenase from2 archaeoglobus fulgidus studied by crystal structure3 analysis and engineering of chimers
16 | d1w0da_ |
|  | 6.8 | 19 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
17 | d1hqsa_ |
|  | 6.7 | 12 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
18 | d1jjga_ |
|  | 6.7 | 38 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
19 | d1n8ja_ |
|  | 6.4 | 23 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
20 | c3blxM_ |
|  | 6.4 | 15 | PDB header:oxidoreductase Chain: M: PDB Molecule:isocitrate dehydrogenase [nad] subunit 1; PDBTitle: yeast isocitrate dehydrogenase (apo form)
21 | c3f7xA_ |
| not modelled | 6.2 | 29 | PDB header:unknown function Chain: A: PDB Molecule:putative polyketide cyclase; PDBTitle: crystal structure of a putative polyketide cyclase (pp0894) from2 pseudomonas putida kt2440 at 1.24 a resolution
22 | c2kilA_ |
| not modelled | 6.2 | 6 | PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: nmr structure of the h103g mutant so2144 h-nox domain from2 shewanella oneidensis in the fe(ii)co ligation state
23 | c3r8wC_ |
| not modelled | 6.1 | 15 | PDB header:oxidoreductase Chain: C: PDB Molecule:3-isopropylmalate dehydrogenase 2, chloroplastic; PDBTitle: structure of 3-isopropylmalate dehydrogenase isoform 2 from2 arabidopsis thaliana at 2.2 angstrom resolution
24 | c3e8vA_ |
| not modelled | 6.1 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:possible transglutaminase-family protein; PDBTitle: crystal structure of a possible transglutaminase-family2 protein proteolytic fragment from bacteroides fragilis
25 | d1a05a_ |
| not modelled | 6.1 | 8 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
26 | c1bknA_ |
| not modelled | 5.9 | 15 | PDB header:dna repair Chain: A: PDB Molecule:mutl; PDBTitle: crystal structure of an n-terminal 40kd fragment of e. coli2 dna mismatch repair protein mutl
27 | d1ydua1 |
| not modelled | 5.9 | 9 | Fold:At5g01610-like Superfamily:At5g01610-like Family:At5g01610-like
28 | d1cm7a_ |
| not modelled | 5.9 | 12 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
29 | c3mhsE_ |
| not modelled | 5.9 | 15 | PDB header:hydrolase/transcription regulator/protei Chain: E: PDB Molecule:saga-associated factor 73; PDBTitle: structure of the saga ubp8/sgf11/sus1/sgf73 dub module bound to2 ubiquitin aldehyde
30 | d3ckma1 |
| not modelled | 5.8 | 13 | Fold:Periplasmic binding protein-like I Superfamily:Periplasmic binding protein-like I Family:L-arabinose binding protein-like
31 | d1luza_ |
| not modelled | 5.8 | 22 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
32 | d1ylea1 |
| not modelled | 5.7 | 6 | Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:AstA-like
33 | c1tyoA_ |
| not modelled | 5.7 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:isocitrate dehydrogenase; PDBTitle: isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix in2 complex with etheno-nadp
34 | d1wpwa_ |
| not modelled | 5.5 | 23 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
35 | d1b25a1 |
| not modelled | 5.5 | 15 | Fold:Aldehyde ferredoxin oxidoreductase, C-terminal domains Superfamily:Aldehyde ferredoxin oxidoreductase, C-terminal domains Family:Aldehyde ferredoxin oxidoreductase, C-terminal domains
36 | c2kk4A_ |
| not modelled | 5.5 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein af_2094; PDBTitle: solution nmr structure of protein af2094 from archaeoglobus2 fulgidus. northeast structural genomics consotium (nesg)3 target gt2
37 | c2op8A_ |
| not modelled | 5.5 | 14 | PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase ywhb; PDBTitle: crystal structure of ywhb- homologue of 4-oxalocrotonate tautomerase
38 | d1m1ha1 |
| not modelled | 5.4 | 46 | Fold:N-utilization substance G protein NusG, insert domain Superfamily:N-utilization substance G protein NusG, insert domain Family:N-utilization substance G protein NusG, insert domain
39 | c1htrP_ |
| not modelled | 5.4 | 29 | PDB header:aspartyl protease Chain: P: PDB Molecule:progastricsin (pro segment); PDBTitle: crystal and molecular structures of human progastricsin at 1.622 angstroms resolution
40 | d1dl6a_ |
| not modelled | 5.3 | 17 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
41 | d1ka1a_ |
| not modelled | 5.3 | 18 | Fold:Carbohydrate phosphatase Superfamily:Carbohydrate phosphatase Family:Inositol monophosphatase/fructose-1,6-bisphosphatase-like
42 | d2q0ia1 |
| not modelled | 5.2 | 22 | Fold:Metallo-hydrolase/oxidoreductase Superfamily:Metallo-hydrolase/oxidoreductase Family:PqsE-like
43 | d1cnza_ |
| not modelled | 5.2 | 12 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
44 | d1yrra2 |
| not modelled | 5.2 | 16 | Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain
45 | c3dbaB_ |
| not modelled | 5.2 | 10 | PDB header:hydrolase Chain: B: PDB Molecule:cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit PDBTitle: crystal structure of the cgmp-bound gaf a domain from the2 photoreceptor phosphodiesterase 6c
46 | d2h6ca2 |
| not modelled | 5.1 | 17 | Fold:Double-stranded beta-helix Superfamily:cAMP-binding domain-like Family:cAMP-binding domain
47 | d1aora1 |
| not modelled | 5.1 | 8 | Fold:Aldehyde ferredoxin oxidoreductase, C-terminal domains Superfamily:Aldehyde ferredoxin oxidoreductase, C-terminal domains Family:Aldehyde ferredoxin oxidoreductase, C-terminal domains
48 | d1g2ua_ |
| not modelled | 5.1 | 12 | Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases
49 | c3hz4A_ |
| not modelled | 5.1 | 11 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: crystal structure of thioredoxin from methanosarcina mazei
50 | d1u55a_ |
| not modelled | 5.1 | 6 | Fold:Ligand-binding domain in the NO signalling and Golgi transport Superfamily:Ligand-binding domain in the NO signalling and Golgi transport Family:H-NOX domain
51 | c2ideE_ |
| not modelled | 5.1 | 25 | PDB header:biosynthetic protein Chain: E: PDB Molecule:molybdenum cofactor biosynthesis protein c; PDBTitle: crystal structure of the molybdenum cofactor biosynthesis protein c2 (ttha1789) from thermus theromophilus hb8

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