Phyre 2 Results for P24200

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Email | l.a.kelley@imperial.ac.uk
Description | P24200
Date | Thu Jan 5 11:41:10 GMT 2012
Unique Job ID | 992fcda1a66e33ca

Summary |

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

Model (left) based on template c2qgpA_
Top template information
PDB header:hydrolase Chain: A: PDB Molecule:hnh endonuclease; PDBTitle: x-ray structure of the nhn endonuclease from geobacter2 metallireducens. northeast structural genomics consortium3 target gmr87.
Confidence and coverage
Confidence: | 98.9% | Coverage: | 28%
77 residues ( 28% of your sequence) have been modelled with 98.9% 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 |

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Sequence |  | M | H | V | F | D | N | N | G | I | E | L | K | A | E | C | S | I | G | E | E | D | G | V | Y | G | L | I | L | E | S | W | G | P | G | D | R | N | K | D | Y | N | I | A | L | D | Y | I | I | E | R | L | V | D | S | G | V | S | Q | V | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  | ? |  |  |  |  |  |  |  | ? |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | V | Y | L | A | S | S | S | V | R | K | H | M | H | S | L | D | E | R | K | I | H | P | G | E | Y | F | T | L | I | G | N | S | P | R | D | I | R | L | K | M | C | G | Y | Q | A | Y | F | S | R | T | G | R | K | E | I | P | S | G | N | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  | ? |  |  |  |  | ? |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | T | K | R | I | L | I | N | V | P | G | I | Y | S | D | S | F | W | A | S | I | I | R | G | E | L | S | E | L | S | Q | P | T | D | D | E | S | L | L | N | M | R | V | S | K | L | I | K | K | T | L | S | Q | P | E | G | S | R | K | P | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | E | V | E | R | L | Q | K | V | Y | V | R | D | P | M | V | K | A | W | I | L | Q | Q | S | K | G | I | C | E | N | C | G | K | N | A | P | F | Y | L | N | D | G | N | P | Y | L | E | V | H | H | V | I | P | L | S | S | G | G | A | D | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | .
Sequence |  | T | D | N | C | V | A | L | C | P | N | C | H | R | E | L | H | Y | S | K | N | A | K | E | L | I | E | M | L | Y | V | N | I | N | R | L | Q | K
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 |
| c2qgpA_ |

### PDB 2qgp chain A

Region: 185 - 268
Aligned: 77
Modelled: 84
Confidence: 98.9%
Identity: 26%
PDB header:hydrolase
Chain: A: PDB Molecule:hnh endonuclease;
PDBTitle: x-ray structure of the nhn endonuclease from geobacter2 metallireducens. northeast structural genomics consortium3 target gmr87.

Phyre2
2 |
| d2gykb1 |

### PDB 2gyk chain B domain 1

Region: 221 - 258
Aligned: 38
Modelled: 38
Confidence: 96.1%
Identity: 34%
Fold: His-Me finger endonucleases
Superfamily: His-Me finger endonucleases
Family: HNH-motif

Phyre2
3 |
| c7ceiB_ |

### PDB 7cei chain B

Region: 221 - 256
Aligned: 36
Modelled: 36
Confidence: 88.4%
Identity: 31%
PDB header:immune system
Chain: B: PDB Molecule:protein (colicin e7 immunity protein);
PDBTitle: the endonuclease domain of colicin e7 in complex with its inhibitor2 im7 protein

Phyre2
4 |
| c2qnfB_ |

### PDB 2qnf chain B

Region: 194 - 255
Aligned: 51
Modelled: 62
Confidence: 82.7%
Identity: 20%
PDB header:hydrolase/dna
Chain: B: PDB Molecule:recombination endonuclease vii;
PDBTitle: crystal structure of t4 endonuclease vii h43n mutant in2 complex with heteroduplex dna containing base mismatches

Phyre2
5 |
| d1e7la2 |

### PDB 1e7l chain A domain 2

Region: 194 - 277
Aligned: 73
Modelled: 84
Confidence: 80.3%
Identity: 22%
Fold: His-Me finger endonucleases
Superfamily: His-Me finger endonucleases
Family: Recombination endonuclease VII, N-terminal domain

Phyre2
6 |
| c2orvB_ |

### PDB 2orv chain B

Region: 204 - 252
Aligned: 38
Modelled: 49
Confidence: 76.1%
Identity: 32%
PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: human thymidine kinase 1 in complex with tp4a

Phyre2
7 |
| c1w4rC_ |

### PDB 1w4r chain C

Region: 204 - 254
Aligned: 40
Modelled: 51
Confidence: 72.2%
Identity: 30%
PDB header:transferase
Chain: C: PDB Molecule:thymidine kinase;
PDBTitle: structure of a type ii thymidine kinase with bound dttp

Phyre2
8 |
| c2b8tA_ |

### PDB 2b8t chain A

Region: 204 - 269
Aligned: 57
Modelled: 66
Confidence: 69.9%
Identity: 26%
PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from u.urealyticum in2 complex with thymidine

Phyre2
9 |
| c2qq0B_ |

### PDB 2qq0 chain B

Region: 204 - 255
Aligned: 41
Modelled: 52
Confidence: 66.5%
Identity: 32%
PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from thermotoga maritima in complex with2 thymidine + appnhp

Phyre2
10 |
| d2jb0b1 |

### PDB 2jb0 chain B domain 1

Region: 221 - 255
Aligned: 34
Modelled: 35
Confidence: 63.0%
Identity: 32%
Fold: His-Me finger endonucleases
Superfamily: His-Me finger endonucleases
Family: HNH-motif

Phyre2
11 |
| d2b8ta2 |

### PDB 2b8t chain A domain 2

Region: 206 - 269
Aligned: 59
Modelled: 64
Confidence: 59.5%
Identity: 22%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Type II thymidine kinase zinc finger

Phyre2
12 |
| d1xbta2 |

### PDB 1xbt chain A domain 2

Region: 206 - 254
Aligned: 38
Modelled: 46
Confidence: 50.8%
Identity: 29%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Type II thymidine kinase zinc finger

Phyre2
13 |
| c3goxB_ |

### PDB 3gox chain B

Region: 151 - 274
Aligned: 91
Modelled: 100
Confidence: 44.7%
Identity: 20%
PDB header:hydrolase/dna
Chain: B: PDB Molecule:restriction endonuclease hpy99i;
PDBTitle: crystal structure of the beta-beta-alpha-me type ii restriction2 endonuclease hpy99i in the absence of edta

Phyre2
14 |
| d1jhfa1 |

### PDB 1jhf chain A domain 1

Region: 44 - 98
Aligned: 50
Modelled: 55
Confidence: 42.6%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: LexA repressor, N-terminal DNA-binding domain

Phyre2
15 |
| c1xx6B_ |

### PDB 1xx6 chain B

Region: 204 - 252
Aligned: 41
Modelled: 49
Confidence: 40.5%
Identity: 24%
PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: x-ray structure of clostridium acetobutylicum thymidine kinase with2 adp. northeast structural genomics target car26.

Phyre2
16 |
| c2iqjB_ |

### PDB 2iqj chain B

Region: 190 - 255
Aligned: 45
Modelled: 45
Confidence: 38.4%
Identity: 31%
PDB header:protein transport
Chain: B: PDB Molecule:stromal membrane-associated protein 1-like;
PDBTitle: crystal structure of the gap domain of smap1l (loc64744)2 stromal membrane-associated protein 1-like

Phyre2
17 |
| c3e2iA_ |

### PDB 3e2i chain A

Region: 204 - 252
Aligned: 40
Modelled: 40
Confidence: 37.7%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from s. aureus

Phyre2
18 |
| c2vr0A_ |

### PDB 2vr0 chain A

Region: 202 - 275
Aligned: 61
Modelled: 74
Confidence: 34.0%
Identity: 20%
PDB header:oxidoreductase
Chain: A: PDB Molecule:cytochrome c nitrite reductase, catalytic subunit nfra;
PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex bound to the hqno inhibitor

Phyre2
19 |
| d1qdba_ |

### PDB 1qdb chain A

Region: 184 - 276
Aligned: 79
Modelled: 93
Confidence: 29.4%
Identity: 24%
Fold: Multiheme cytochromes
Superfamily: Multiheme cytochromes
Family: Di-heme elbow motif

Phyre2
20 |
| c1tvtA_ |

### PDB 1tvt chain A

Region: 160 - 227
Aligned: 49
Modelled: 57
Confidence: 27.3%
Identity: 22%
PDB header:transcription regulation
Chain: A: PDB Molecule:transactivator protein;
PDBTitle: structure of the equine infectious anemia virus tat protein

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2qgpA_ |
|  | 98.9 | 26 | PDB header:hydrolase Chain: A: PDB Molecule:hnh endonuclease; PDBTitle: x-ray structure of the nhn endonuclease from geobacter2 metallireducens. northeast structural genomics consortium3 target gmr87.
2 | d2gykb1 |
|  | 96.1 | 34 | Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif
3 | c7ceiB_ |
|  | 88.4 | 31 | PDB header:immune system Chain: B: PDB Molecule:protein (colicin e7 immunity protein); PDBTitle: the endonuclease domain of colicin e7 in complex with its inhibitor2 im7 protein
4 | c2qnfB_ |
|  | 82.7 | 20 | PDB header:hydrolase/dna Chain: B: PDB Molecule:recombination endonuclease vii; PDBTitle: crystal structure of t4 endonuclease vii h43n mutant in2 complex with heteroduplex dna containing base mismatches
5 | d1e7la2 |
|  | 80.3 | 22 | Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Recombination endonuclease VII, N-terminal domain
6 | c2orvB_ |
|  | 76.1 | 32 | PDB header:transferase Chain: B: PDB Molecule:thymidine kinase; PDBTitle: human thymidine kinase 1 in complex with tp4a
7 | c1w4rC_ |
|  | 72.2 | 30 | PDB header:transferase Chain: C: PDB Molecule:thymidine kinase; PDBTitle: structure of a type ii thymidine kinase with bound dttp
8 | c2b8tA_ |
|  | 69.9 | 26 | PDB header:transferase Chain: A: PDB Molecule:thymidine kinase; PDBTitle: crystal structure of thymidine kinase from u.urealyticum in2 complex with thymidine
9 | c2qq0B_ |
|  | 66.5 | 32 | PDB header:transferase Chain: B: PDB Molecule:thymidine kinase; PDBTitle: thymidine kinase from thermotoga maritima in complex with2 thymidine + appnhp
10 | d2jb0b1 |
|  | 63.0 | 32 | Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif
11 | d2b8ta2 |
|  | 59.5 | 22 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Type II thymidine kinase zinc finger
12 | d1xbta2 |
|  | 50.8 | 29 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Type II thymidine kinase zinc finger
13 | c3goxB_ |
|  | 44.7 | 20 | PDB header:hydrolase/dna Chain: B: PDB Molecule:restriction endonuclease hpy99i; PDBTitle: crystal structure of the beta-beta-alpha-me type ii restriction2 endonuclease hpy99i in the absence of edta
14 | d1jhfa1 |
|  | 42.6 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain
15 | c1xx6B_ |
|  | 40.5 | 24 | PDB header:transferase Chain: B: PDB Molecule:thymidine kinase; PDBTitle: x-ray structure of clostridium acetobutylicum thymidine kinase with2 adp. northeast structural genomics target car26.
16 | c2iqjB_ |
|  | 38.4 | 31 | PDB header:protein transport Chain: B: PDB Molecule:stromal membrane-associated protein 1-like; PDBTitle: crystal structure of the gap domain of smap1l (loc64744)2 stromal membrane-associated protein 1-like
17 | c3e2iA_ |
|  | 37.7 | 20 | PDB header:transferase Chain: A: PDB Molecule:thymidine kinase; PDBTitle: crystal structure of thymidine kinase from s. aureus
18 | c2vr0A_ |
|  | 34.0 | 20 | PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c nitrite reductase, catalytic subunit nfra; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex bound to the hqno inhibitor
19 | d1qdba_ |
|  | 29.4 | 24 | Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Di-heme elbow motif
20 | c1tvtA_ |
|  | 27.3 | 22 | PDB header:transcription regulation Chain: A: PDB Molecule:transactivator protein; PDBTitle: structure of the equine infectious anemia virus tat protein
21 | c3h7hA_ |
| not modelled | 24.2 | 26 | PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt4; PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273)
22 | d1vp8a_ |
| not modelled | 23.8 | 28 | Fold:Pyruvate kinase C-terminal domain-like Superfamily:PK C-terminal domain-like Family:MTH1675-like
23 | d2dj7a1 |
| not modelled | 23.3 | 33 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
24 | c3lvrE_ |
| not modelled | 23.1 | 36 | PDB header:protein transport Chain: E: PDB Molecule:arf-gap with sh3 domain, ank repeat and ph domain- PDBTitle: the crystal structure of asap3 in complex with arf6 in transition2 state soaked with calcium
25 | c2ju5A_ |
| not modelled | 22.0 | 16 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin disulfide isomerase; PDBTitle: dsbh oxidoreductase
26 | c2p57A_ |
| not modelled | 21.7 | 29 | PDB header:metal binding protein Chain: A: PDB Molecule:gtpase-activating protein znf289; PDBTitle: gap domain of znf289, an id1-regulated zinc finger protein
27 | d2glia5 |
| not modelled | 21.5 | 46 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
28 | d1jx6a_ |
| not modelled | 21.5 | 22 | Fold:Periplasmic binding protein-like I Superfamily:Periplasmic binding protein-like I Family:L-arabinose binding protein-like
29 | c2wy3B_ |
| not modelled | 21.0 | 48 | PDB header:immune system/viral protein Chain: B: PDB Molecule:uncharacterized protein ul16; PDBTitle: structure of the hcmv ul16-micb complex elucidates select2 binding of a viral immunoevasin to diverse nkg2d ligands
30 | c2f3oB_ |
| not modelled | 20.2 | 24 | PDB header:unknown function Chain: B: PDB Molecule:pyruvate formate-lyase 2; PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus
31 | d1xx6a2 |
| not modelled | 19.8 | 29 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Type II thymidine kinase zinc finger
32 | c3hcwB_ |
| not modelled | 19.8 | 25 | PDB header:rna binding protein Chain: B: PDB Molecule:maltose operon transcriptional repressor; PDBTitle: crystal structure of probable maltose operon transcriptional repressor2 malr from staphylococcus areus
33 | c2ja1A_ |
| not modelled | 19.3 | 21 | PDB header:transferase Chain: A: PDB Molecule:thymidine kinase; PDBTitle: thymidine kinase from b. cereus with ttp bound as phosphate2 donor.
34 | c3m7kA_ |
| not modelled | 18.9 | 22 | PDB header:hydrolase/dna Chain: A: PDB Molecule:restriction endonuclease paci; PDBTitle: crystal structure of paci-dna enzyme product complex
35 | c3na7A_ |
| not modelled | 17.9 | 34 | PDB header:gene regulation, chaperone Chain: A: PDB Molecule:hp0958; PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
36 | d1x3ha2 |
| not modelled | 17.7 | 35 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
37 | d2jnea1 |
| not modelled | 17.5 | 54 | Fold:Rubredoxin-like Superfamily:YfgJ-like Family:YfgJ-like
38 | c2jneA_ |
| not modelled | 17.5 | 54 | PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein yfgj; PDBTitle: nmr structure of e.coli yfgj modelled with two zn+2 bound.2 northeast structural genomics consortium target er317.
39 | c3iraA_ |
| not modelled | 17.1 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein; PDBTitle: the crystal structure of one domain of the conserved protein from2 methanosarcina mazei go1
40 | c1yshD_ |
| not modelled | 16.9 | 53 | PDB header:structural protein/rna Chain: D: PDB Molecule:ribosomal protein l37a; PDBTitle: localization and dynamic behavior of ribosomal protein l30e
41 | d1jj2y_ |
| not modelled | 16.5 | 26 | Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae
42 | d1r9da_ |
| not modelled | 16.1 | 22 | Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like
43 | c2x41A_ |
| not modelled | 16.1 | 42 | PDB header:hydrolase Chain: A: PDB Molecule:beta-glucosidase; PDBTitle: structure of beta-glucosidase 3b from thermotoga neapolitana2 in complex with glucose
44 | c2d9lA_ |
| not modelled | 16.0 | 24 | PDB header:gene regulation Chain: A: PDB Molecule:nucleoporin-like protein rip; PDBTitle: solution structure of the arfgap domain of human rip
45 | c2zkrz_ |
| not modelled | 16.0 | 41 | PDB header:ribosomal protein/rna Chain: Z: PDB Molecule:e site t-rna; 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
46 | c2j7aE_ |
| not modelled | 15.3 | 18 | PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c nitrite reductase nrfa; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex from desulfovibrio vulgaris
47 | c2jrpA_ |
| not modelled | 15.2 | 46 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cytoplasmic protein; PDBTitle: solution nmr structure of yfgj from salmonella typhimurium2 modeled with two zn+2 bound, northeast structural genomics3 consortium target str86
48 | c3dwdB_ |
| not modelled | 15.0 | 31 | PDB header:transport protein Chain: B: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1; PDBTitle: crystal structure of the arfgap domain of human arfgap1
49 | d1vqoz1 |
| not modelled | 14.8 | 21 | Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae
50 | c1fs9A_ |
| not modelled | 14.7 | 33 | PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c nitrite reductase; PDBTitle: cytochrome c nitrite reductase from wolinella succinogenes-azide2 complex
51 | c2b0oF_ |
| not modelled | 14.5 | 38 | PDB header:metal binding protein Chain: F: PDB Molecule:uplc1; PDBTitle: crystal structure of uplc1 gap domain
52 | c2joxA_ |
| not modelled | 14.1 | 28 | PDB header:transcription Chain: A: PDB Molecule:churchill protein; PDBTitle: embryonic neural inducing factor churchill is not a dna-2 binding zinc finger protein: solution structure reveals a3 solvent-exposed beta-sheet and zinc binuclear cluster
53 | c1i6hA_ |
| not modelled | 14.0 | 17 | PDB header:transcription/dna-rna hybrid Chain: A: PDB Molecule:dna-directed rna polymerase ii largest subunit; PDBTitle: rna polymerase ii elongation complex
54 | d2ic1a1 |
| not modelled | 13.9 | 26 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Cysteine dioxygenase type I
55 | c3qqcA_ |
| not modelled | 13.8 | 21 | PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase subunit b, dna-directed rna PDBTitle: crystal structure of archaeal spt4/5 bound to the rnap clamp domain
56 | d3elna1 |
| not modelled | 13.6 | 26 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Cysteine dioxygenase type I
57 | c2y8nC_ |
| not modelled | 13.5 | 20 | PDB header:lyase Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit; PDBTitle: crystal structure of glycyl radical enzyme
58 | d1fs7a_ |
| not modelled | 13.3 | 33 | Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Di-heme elbow motif
59 | c3cc4Z_ |
| not modelled | 13.3 | 24 | PDB header:ribosome Chain: Z: PDB Molecule:50s ribosomal protein l37ae; PDBTitle: co-crystal structure of anisomycin bound to the 50s ribosomal subunit
60 | c4a17Y_ |
| not modelled | 13.2 | 47 | PDB header:ribosome Chain: Y: PDB Molecule:rpl37a; 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 2.
61 | d1vh3a_ |
| not modelled | 12.8 | 21 | Fold:Nucleotide-diphospho-sugar transferases Superfamily:Nucleotide-diphospho-sugar transferases Family:Cytidylytransferase
62 | d1ubdc1 |
| not modelled | 12.6 | 50 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
63 | d1weoa_ |
| not modelled | 12.5 | 21 | Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4
64 | d1ffkw_ |
| not modelled | 12.4 | 19 | Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae
65 | d1inza_ |
| not modelled | 11.6 | 31 | Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:ENTH domain
66 | c3f9uA_ |
| not modelled | 11.1 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative exported cytochrome c biogenesis-related protein; PDBTitle: crystal structure of c-terminal domain of putative exported cytochrome2 c biogenesis-related protein from bacteroides fragilis
67 | d1twfa_ |
| not modelled | 10.9 | 17 | Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase Family:RNA-polymerase beta-prime
68 | c3jyw9_ |
| not modelled | 10.9 | 29 | PDB header:ribosome Chain: 9: PDB Molecule:60s ribosomal protein l43; PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution
69 | c1rikA_ |
| not modelled | 10.6 | 38 | PDB header:de novo protein Chain: A: PDB Molecule:e6apc1 peptide; PDBTitle: e6-binding zinc finger (e6apc1)
70 | d1hs5a_ |
| not modelled | 10.6 | 100 | Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain
71 | d1n5ga_ |
| not modelled | 10.5 | 33 | Fold:Zinc finger domain of DNA polymerase-alpha Superfamily:Zinc finger domain of DNA polymerase-alpha Family:Zinc finger domain of DNA polymerase-alpha
72 | d2fiya1 |
| not modelled | 10.4 | 32 | Fold:FdhE-like Superfamily:FdhE-like Family:FdhE-like
73 | c1x4lA_ |
| not modelled | 10.2 | 28 | PDB header:metal binding protein Chain: A: PDB Molecule:skeletal muscle lim-protein 3; PDBTitle: solution structure of lim domain in four and a half lim2 domains protein 2
74 | c3cueH_ |
| not modelled | 9.9 | 25 | PDB header:protein transport Chain: H: PDB Molecule:transport protein particle 31 kda subunit; PDBTitle: crystal structure of a trapp subassembly activating the rab2 ypt1p
75 | c2qu7B_ |
| not modelled | 9.8 | 21 | PDB header:transcription Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of a putative transcription regulator2 from staphylococcus saprophyticus subsp. saprophyticus
76 | d1h16a_ |
| not modelled | 9.6 | 20 | Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like
77 | c2l4zA_ |
| not modelled | 9.5 | 26 | PDB header:hydrolase, metal binding protein Chain: A: PDB Molecule:dna endonuclease rbbp8, lim domain transcription factor PDBTitle: nmr structure of fusion of ctip (641-685) to lmo4-lim1 (18-82)
78 | c3pnnA_ |
| not modelled | 9.2 | 22 | PDB header:transferase Chain: A: PDB Molecule:conserved domain protein; PDBTitle: the crystal structure of a glycosyltransferase from porphyromonas2 gingivalis w83
79 | c3c3kA_ |
| not modelled | 9.1 | 20 | PDB header:isomerase Chain: A: PDB Molecule:alanine racemase; PDBTitle: crystal structure of an uncharacterized protein from actinobacillus2 succinogenes
80 | c3gbvB_ |
| not modelled | 9.1 | 13 | PDB header:transcription regulator Chain: B: PDB Molecule:putative laci-family transcriptional regulator; PDBTitle: crystal structure of a putative laci transcriptional regulator from2 bacteroides fragilis
81 | c1m3vA_ |
| not modelled | 9.1 | 15 | PDB header:metal binding protein Chain: A: PDB Molecule:fusion of the lim interacting domain of ldb1 and PDBTitle: flin4: fusion of the lim binding domain of ldb1 and the n-2 terminal lim domain of lmo4
82 | c3o47A_ |
| not modelled | 9.1 | 28 | PDB header:hydrolase, hydrolase activator Chain: A: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1, adp- PDBTitle: crystal structure of arfgap1-arf1 fusion protein
83 | c3jywY_ |
| not modelled | 9.0 | 38 | PDB header:ribosome Chain: Y: PDB Molecule:60s ribosomal protein l37(a); PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution
84 | c2qh8A_ |
| not modelled | 8.9 | 10 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of conserved domain protein from vibrio2 cholerae o1 biovar eltor str. n16961
85 | c1b8tA_ |
| not modelled | 8.9 | 32 | PDB header:contractile Chain: A: PDB Molecule:protein (crp1); PDBTitle: solution structure of the chicken crp1
86 | c1vhkA_ |
| not modelled | 8.8 | 24 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein yqeu; PDBTitle: crystal structure of an hypothetical protein
87 | c3fxhA_ |
| not modelled | 8.8 | 58 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:integron gene cassette protein hfx_cass2; PDBTitle: crystal structure from the mobile metagenome of halifax2 harbour sewage outfall: integron cassette protein hfx_cass2
88 | c2zkr2_ |
| not modelled | 8.7 | 38 | PDB header:ribosomal protein/rna Chain: 2: PDB Molecule:60s ribosomal protein l37e; 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
89 | c2r5iL_ |
| not modelled | 8.7 | 33 | PDB header:viral protein Chain: L: PDB Molecule:l1 protein; PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 18
90 | c2o20H_ |
| not modelled | 8.5 | 30 | PDB header:transcription Chain: H: PDB Molecule:catabolite control protein a; PDBTitle: crystal structure of transcription regulator ccpa of lactococcus2 lactis
91 | c3ac0B_ |
| not modelled | 8.4 | 35 | PDB header:hydrolase Chain: B: PDB Molecule:beta-glucosidase i; PDBTitle: crystal structure of beta-glucosidase from kluyveromyces marxianus in2 complex with glucose
92 | c1s1iY_ |
| not modelled | 8.3 | 38 | PDB header:ribosome Chain: Y: PDB Molecule:60s ribosomal protein l37-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.
93 | d1qcva_ |
| not modelled | 8.3 | 20 | Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Rubredoxin
94 | c3gn5B_ |
| not modelled | 8.3 | 15 | PDB header:dna binding protein Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021); PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
95 | c3mizB_ |
| not modelled | 8.1 | 14 | PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator protein, laci PDBTitle: crystal structure of a putative transcriptional regulator2 protein, lacl family from rhizobium etli
96 | d2yt9a2 |
| not modelled | 8.0 | 83 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
97 | c3e56A_ |
| not modelled | 8.0 | 19 | PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the 2.0 angstrom resolution crystal structure of npr1517, a putative2 heterocyst differentiation inhibitor from nostoc punctiforme
98 | d2dlqa4 |
| not modelled | 7.8 | 67 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
99 | c1tjlD_ |
| not modelled | 7.8 | 56 | PDB header:transcription Chain: D: PDB Molecule:dnak suppressor protein; PDBTitle: crystal structure of transcription factor dksa from e. coli

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