Phyre 2 Results for P50465

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Email | l.a.kelley@imperial.ac.uk
Description | P50465
Date | Thu Jan 5 12:04:46 GMT 2012
Unique Job ID | e5ec7f8e4f23070d

Summary |

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

Model (left) based on template c2opfA_
Top template information
PDB header:hydrolase/dna Chain: A: PDB Molecule:endonuclease viii; PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
Confidence and coverage
Confidence: | 100.0% | Coverage: | 97%
256 residues ( 97% 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 | P | E | G | P | E | I | R | R | A | A | D | N | L | E | A | A | I | K | G | K | P | L | T | D | V | W | F | A | F | P | Q | L | K | P | Y | Q | S | Q | L | I | G | Q | H | V | T | H | V | E | T | R | G | K | A | L | L | T | H | F | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | N | D | L | T | L | Y | S | H | N | Q | L | Y | G | V | W | R | V | V | D | T | G | E | E | P | Q | T | T | R | V | L | R | V | K | L | Q | T | A | D | K | T | I | L | L | Y | S | A | S | D | I | E | M | L | T | P | E | Q | L | T | T | H
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | P | F | L | Q | R | V | G | P | D | V | L | D | P | N | L | T | P | E | V | V | K | E | R | L | L | S | P | R | F | R | N | R | Q | F | A | G | L | L | L | D | Q | A | F | L | A | G | L | G | N | Y | L | R | V | E | I | L | W | Q | V | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | L | T | G | N | H | K | A | K | D | L | N | A | A | Q | L | D | A | L | A | H | A | L | L | E | I | P | R | F | S | Y | A | T | R | G | Q | V | D | E | N | K | H | H | G | A | L | F | R | F | K | V | F | H | R | D | G | E | P | C | E | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | .
Sequence |  | C | G | S | I | I | E | K | T | T | L | S | S | R | P | F | Y | W | C | P | G | C | Q | H
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 |
| c2opfA_ |

### PDB 2opf chain A

Region: 2 - 263
Aligned: 256
Modelled: 256
Confidence: 100.0%
Identity: 98%
PDB header:hydrolase/dna
Chain: A: PDB Molecule:endonuclease viii;
PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate

Phyre2
2 |
| c2f5qA_ |

### PDB 2f5q chain A

Region: 2 - 262
Aligned: 255
Modelled: 261
Confidence: 100.0%
Identity: 30%
PDB header:hydrolase/dna
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase;
PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2

Phyre2
3 |
| c1nnjA_ |

### PDB 1nnj chain A

Region: 3 - 262
Aligned: 255
Modelled: 260
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna

Phyre2
4 |
| c1k82D_ |

### PDB 1k82 chain D

Region: 2 - 262
Aligned: 253
Modelled: 261
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna

Phyre2
5 |
| c1ee8A_ |

### PDB 1ee8 chain A

Region: 2 - 262
Aligned: 251
Modelled: 261
Confidence: 100.0%
Identity: 27%
PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8

Phyre2
6 |
| c3a46B_ |

### PDB 3a46 chain B

Region: 2 - 262
Aligned: 247
Modelled: 261
Confidence: 100.0%
Identity: 26%
PDB header:hydrolase
Chain: B: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of mvnei1/thf complex

Phyre2
7 |
| c1tdhA_ |

### PDB 1tdh chain A

Region: 2 - 257
Aligned: 238
Modelled: 249
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:nei endonuclease viii-like 1;
PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1)

Phyre2
8 |
| d1k3xa1 |

### PDB 1k3x chain A domain 1

Region: 126 - 214
Aligned: 89
Modelled: 89
Confidence: 100.0%
Identity: 100%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Middle domain of MutM-like DNA repair proteins

Phyre2
9 |
| d1k3xa2 |

### PDB 1k3x chain A domain 2

Region: 2 - 125
Aligned: 124
Modelled: 124
Confidence: 100.0%
Identity: 98%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2
10 |
| d1r2za1 |

### PDB 1r2z chain A domain 1

Region: 127 - 222
Aligned: 93
Modelled: 96
Confidence: 100.0%
Identity: 27%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Middle domain of MutM-like DNA repair proteins

Phyre2
11 |
| d1k82a1 |

### PDB 1k82 chain A domain 1

Region: 127 - 217
Aligned: 88
Modelled: 91
Confidence: 100.0%
Identity: 22%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Middle domain of MutM-like DNA repair proteins

Phyre2
12 |
| d1ee8a1 |

### PDB 1ee8 chain A domain 1

Region: 127 - 218
Aligned: 89
Modelled: 92
Confidence: 100.0%
Identity: 28%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Middle domain of MutM-like DNA repair proteins

Phyre2
13 |
| d1tdza1 |

### PDB 1tdz chain A domain 1

Region: 127 - 216
Aligned: 87
Modelled: 90
Confidence: 100.0%
Identity: 25%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Middle domain of MutM-like DNA repair proteins

Phyre2
14 |
| d1r2za2 |

### PDB 1r2z chain A domain 2

Region: 2 - 126
Aligned: 122
Modelled: 125
Confidence: 99.9%
Identity: 27%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2
15 |
| d1ee8a2 |

### PDB 1ee8 chain A domain 2

Region: 2 - 126
Aligned: 117
Modelled: 125
Confidence: 99.9%
Identity: 25%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2
16 |
| d1tdza2 |

### PDB 1tdz chain A domain 2

Region: 3 - 126
Aligned: 122
Modelled: 124
Confidence: 99.9%
Identity: 20%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2
17 |
| d1k82a2 |

### PDB 1k82 chain A domain 2

Region: 2 - 126
Aligned: 122
Modelled: 122
Confidence: 99.9%
Identity: 22%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2
18 |
| d1tdha1 |

### PDB 1tdh chain A domain 1

Region: 126 - 207
Aligned: 82
Modelled: 82
Confidence: 99.8%
Identity: 30%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Middle domain of MutM-like DNA repair proteins

Phyre2
19 |
| d1tdha2 |

### PDB 1tdh chain A domain 2

Region: 2 - 108
Aligned: 106
Modelled: 107
Confidence: 99.8%
Identity: 20%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2
20 |
| d2hkja1 |

### PDB 2hkj chain A domain 1

Region: 126 - 205
Aligned: 75
Modelled: 80
Confidence: 99.6%
Identity: 20%
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Family: Topoisomerase VI-B subunit middle domain

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2opfA_ |
|  | 100.0 | 98 | PDB header:hydrolase/dna Chain: A: PDB Molecule:endonuclease viii; PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
2 | c2f5qA_ |
|  | 100.0 | 30 | PDB header:hydrolase/dna Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase; PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2
3 | c1nnjA_ |
|  | 100.0 | 24 | PDB header:hydrolase Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna
4 | c1k82D_ |
|  | 100.0 | 24 | PDB header:hydrolase/dna Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna
5 | c1ee8A_ |
|  | 100.0 | 27 | PDB header:dna binding protein Chain: A: PDB Molecule:mutm (fpg) protein; PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
6 | c3a46B_ |
|  | 100.0 | 26 | PDB header:hydrolase Chain: B: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of mvnei1/thf complex
7 | c1tdhA_ |
|  | 100.0 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:nei endonuclease viii-like 1; PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1)
8 | d1k3xa1 |
|  | 100.0 | 100 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
9 | d1k3xa2 |
|  | 100.0 | 98 | Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins
10 | d1r2za1 |
|  | 100.0 | 27 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
11 | d1k82a1 |
|  | 100.0 | 22 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
12 | d1ee8a1 |
|  | 100.0 | 28 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
13 | d1tdza1 |
|  | 100.0 | 25 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
14 | d1r2za2 |
|  | 99.9 | 27 | Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins
15 | d1ee8a2 |
|  | 99.9 | 25 | Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins
16 | d1tdza2 |
|  | 99.9 | 20 | Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins
17 | d1k82a2 |
|  | 99.9 | 22 | Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins
18 | d1tdha1 |
|  | 99.8 | 30 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins
19 | d1tdha2 |
|  | 99.8 | 20 | Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins
20 | d2hkja1 |
|  | 99.6 | 20 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Topoisomerase VI-B subunit middle domain
21 | d1k3xa3 |
| not modelled | 99.5 | 100 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
22 | d1ee8a3 |
| not modelled | 99.5 | 32 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
23 | d1tdza3 |
| not modelled | 99.5 | 34 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
24 | d1r2za3 |
| not modelled | 99.5 | 42 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
25 | d1k82a3 |
| not modelled | 99.5 | 36 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
26 | d1l1ta3 |
| not modelled | 99.4 | 46 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
27 | d2uubm1 |
| not modelled | 96.8 | 24 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13
28 | c2zkqm_ |
| not modelled | 96.6 | 14 | PDB header:ribosomal protein/rna Chain: M: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
29 | c3iz6M_ |
| not modelled | 96.5 | 20 | PDB header:ribosome Chain: M: PDB Molecule:40s ribosomal protein s18 (s13p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
30 | d1i94m_ |
| not modelled | 96.4 | 27 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13
31 | d2gy9m1 |
| not modelled | 96.4 | 24 | Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13
32 | c2xznM_ |
| not modelled | 96.3 | 20 | PDB header:ribosome Chain: M: PDB Molecule:rps18e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2
33 | c3doaA_ |
| not modelled | 96.1 | 19 | PDB header:protein binding Chain: A: PDB Molecule:fibrinogen binding protein; PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus
34 | d2i0za2 |
| not modelled | 94.0 | 21 | Fold:HI0933 insert domain-like Superfamily:HI0933 insert domain-like Family:HI0933 insert domain-like
35 | c1mx0D_ |
| not modelled | 93.6 | 18 | PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit
36 | d1qyra_ |
| not modelled | 90.9 | 28 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:rRNA adenine dimethylase-like
37 | c2gb5B_ |
| not modelled | 88.3 | 20 | PDB header:hydrolase Chain: B: PDB Molecule:nadh pyrophosphatase; PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution
38 | c3uzuA_ |
| not modelled | 88.1 | 24 | PDB header:transferase Chain: A: PDB Molecule:ribosomal rna small subunit methyltransferase a; PDBTitle: the structure of the ribosomal rna small subunit methyltransferase a2 from burkholderia pseudomallei
39 | c3fuxB_ |
| not modelled | 85.3 | 20 | PDB header:transferase Chain: B: PDB Molecule:dimethyladenosine transferase; PDBTitle: t. thermophilus 16s rrna a1518 and a1519 methyltransferase (ksga) in2 complex with 5'-methylthioadenosine in space group p212121
40 | c3fteA_ |
| not modelled | 85.3 | 15 | PDB header:transferase/rna Chain: A: PDB Molecule:dimethyladenosine transferase; PDBTitle: crystal structure of a. aeolicus ksga in complex with rna
41 | c1yuzB_ |
| not modelled | 85.0 | 17 | PDB header:oxidoreductase Chain: B: PDB Molecule:nigerythrin; PDBTitle: partially reduced state of nigerythrin
42 | c3tqsB_ |
| not modelled | 82.1 | 9 | PDB header:transferase Chain: B: PDB Molecule:ribosomal rna small subunit methyltransferase a; PDBTitle: structure of the dimethyladenosine transferase (ksga) from coxiella2 burnetii
43 | c3bbnM_ |
| not modelled | 78.7 | 23 | PDB header:ribosome Chain: M: PDB Molecule:ribosomal protein s13; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome.
44 | d2fiya1 |
| not modelled | 78.1 | 23 | Fold:FdhE-like Superfamily:FdhE-like Family:FdhE-like
45 | c1dvbA_ |
| not modelled | 77.4 | 20 | PDB header:electron transport Chain: A: PDB Molecule:rubrerythrin; PDBTitle: rubrerythrin
46 | d1twfi2 |
| not modelled | 74.7 | 29 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
47 | d2gqfa2 |
| not modelled | 74.4 | 15 | Fold:HI0933 insert domain-like Superfamily:HI0933 insert domain-like Family:HI0933 insert domain-like
48 | c2jneA_ |
| not modelled | 74.0 | 17 | 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.
49 | d2jnea1 |
| not modelled | 74.0 | 17 | Fold:Rubredoxin-like Superfamily:YfgJ-like Family:YfgJ-like
50 | c2jrpA_ |
| not modelled | 73.5 | 17 | 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
51 | d2f4ma1 |
| not modelled | 73.4 | 16 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core
52 | c3u50C_ |
| not modelled | 70.8 | 27 | PDB header:dna binding protein Chain: C: PDB Molecule:telomerase-associated protein 82; PDBTitle: crystal structure of the tetrahymena telomerase processivity factor2 teb1 ob-c
53 | d2akla2 |
| not modelled | 70.5 | 42 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:PhnA zinc-binding domain
54 | d1qypa_ |
| not modelled | 69.9 | 32 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
55 | c2owoA_ |
| not modelled | 65.1 | 38 | PDB header:ligase/dna Chain: A: PDB Molecule:dna ligase; PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate
56 | c2hr5B_ |
| not modelled | 62.7 | 29 | PDB header:metal binding protein Chain: B: PDB Molecule:rubrerythrin; PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form
57 | d1pfta_ |
| not modelled | 61.8 | 28 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
58 | c3eg9B_ |
| not modelled | 61.7 | 23 | PDB header:protein transport Chain: B: PDB Molecule:sec24 related gene family, member d; PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23/24 bound to the transport signal sequence of membrin
59 | c2kpiA_ |
| not modelled | 61.6 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sco3027; PDBTitle: solution nmr structure of streptomyces coelicolor sco30272 modeled with zn+2 bound, northeast structural genomics3 consortium target rr58
60 | d1l1oc_ |
| not modelled | 61.4 | 23 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB
61 | c3egxB_ |
| not modelled | 61.2 | 29 | PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24a; PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23a/24a complexed with the snare protein sec22b and3 bound to the transport signal sequence of the snare protein4 bet1
62 | c2h1rA_ |
| not modelled | 61.0 | 11 | PDB header:transferase Chain: A: PDB Molecule:dimethyladenosine transferase, putative; PDBTitle: crystal structure of a dimethyladenosine transferase from2 plasmodium falciparum
63 | c1dgsB_ |
| not modelled | 60.8 | 35 | PDB header:ligase Chain: B: PDB Molecule:dna ligase; PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis
64 | c1pd0A_ |
| not modelled | 60.7 | 27 | PDB header:transport protein Chain: A: PDB Molecule:protein transport protein sec24; PDBTitle: crystal structure of the copii coat subunit, sec24,2 complexed with a peptide from the snare protein sed53 (yeast syntaxin-5)
65 | c2lcqA_ |
| not modelled | 60.1 | 30 | PDB header:metal binding protein Chain: A: PDB Molecule:putative toxin vapc6; PDBTitle: solution structure of the endonuclease nob1 from p.horikoshii
66 | d1tfia_ |
| not modelled | 59.7 | 30 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
67 | d1qf8a_ |
| not modelled | 59.5 | 30 | Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit
68 | d1odha_ |
| not modelled | 57.7 | 13 | Fold:GCM domain Superfamily:GCM domain Family:GCM domain
69 | c3h0gI_ |
| not modelled | 57.6 | 28 | PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9; PDBTitle: rna polymerase ii from schizosaccharomyces pombe
70 | c3eh2B_ |
| not modelled | 55.8 | 19 | PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24c; PDBTitle: crystal structure of the human copii-coat protein sec24c
71 | c1m2vB_ |
| not modelled | 54.9 | 27 | PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24; PDBTitle: crystal structure of the yeast sec23/24 heterodimer
72 | c1i3qI_ |
| not modelled | 53.4 | 29 | PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution
73 | c2js4A_ |
| not modelled | 53.0 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0434 protein bb2007; PDBTitle: solution nmr structure of bordetella bronchiseptica protein2 bb2007. northeast structural genomics consortium target3 bor54
74 | c3na7A_ |
| not modelled | 52.5 | 24 | PDB header:gene regulation, chaperone Chain: A: PDB Molecule:hp0958; PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
75 | d1x3za1 |
| not modelled | 52.2 | 22 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core
76 | c2zbkB_ |
| not modelled | 52.1 | 18 | PDB header:isomerase Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b; PDBTitle: crystal structure of an intact type ii dna topoisomerase:2 insights into dna transfer mechanisms
77 | c2jr6A_ |
| not modelled | 51.6 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0434 protein nma0874; PDBTitle: solution structure of upf0434 protein nma0874. northeast structural2 genomics target mr32
78 | c1m2oA_ |
| not modelled | 51.3 | 23 | PDB header:protein transport/signaling protein Chain: A: PDB Molecule:protein transport protein sec23; PDBTitle: crystal structure of the sec23-sar1 complex
79 | c2riqA_ |
| not modelled | 50.7 | 25 | PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: crystal structure of the third zinc-binding domain of human parp-1
80 | d2ct7a1 |
| not modelled | 50.1 | 21 | Fold:RING/U-box Superfamily:RING/U-box Family:IBR domain
81 | d1pd0a5 |
| not modelled | 49.8 | 27 | Fold:Rubredoxin-like Superfamily:Zn-finger domain of Sec23/24 Family:Zn-finger domain of Sec23/24
82 | d2avue1 |
| not modelled | 49.1 | 20 | Fold:FlhC-like Superfamily:FlhC-like Family:FlhC-like
83 | c2jvnA_ |
| not modelled | 48.7 | 21 | PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: domain c of human parp-1
84 | c3eswA_ |
| not modelled | 46.1 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine PDBTitle: complex of yeast pngase with glcnac2-iac.
85 | c2avuF_ |
| not modelled | 45.0 | 20 | PDB header:transcription activator Chain: F: PDB Molecule:flagellar transcriptional activator flhc; PDBTitle: structure of the escherichia coli flhdc complex, a2 prokaryotic heteromeric regulator of transcription
86 | d2jnya1 |
| not modelled | 44.5 | 13 | Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like
87 | c2ba1B_ |
| not modelled | 44.1 | 23 | PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core
88 | d1u5ka2 |
| not modelled | 43.8 | 21 | Fold:ArfGap/RecO-like zinc finger Superfamily:ArfGap/RecO-like zinc finger Family:RecO C-terminal domain-like
89 | c3kp9A_ |
| not modelled | 43.1 | 67 | PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase
90 | d2b9da1 |
| not modelled | 42.7 | 28 | Fold:E7 C-terminal domain-like Superfamily:E7 C-terminal domain-like Family:E7 C-terminal domain-like
91 | c1u5kA_ |
| not modelled | 41.6 | 23 | PDB header:recombination,replication Chain: A: PDB Molecule:hypothetical protein; PDBTitle: recombinational repair protein reco
92 | d2k4xa1 |
| not modelled | 41.6 | 32 | Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein S27a
93 | d1ctla1 |
| not modelled | 41.5 | 33 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
94 | d1ibia1 |
| not modelled | 39.3 | 50 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
95 | d1wd2a_ |
| not modelled | 39.3 | 27 | Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4
96 | d1dl6a_ |
| not modelled | 39.2 | 22 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
97 | c1nypA_ |
| not modelled | 39.1 | 23 | PDB header:cell adhesion Chain: A: PDB Molecule:pinch protein; PDBTitle: 4th lim domain of pinch protein
98 | c3d00A_ |
| not modelled | 39.0 | 23 | PDB header:metal binding protein Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase subunit e; PDBTitle: crystal structure of a tungsten formylmethanofuran dehydrogenase2 subunit e (fmde)-like protein (syn_00638) from syntrophus3 aciditrophicus at 1.90 a resolution
99 | d2pk7a1 |
| not modelled | 38.3 | 13 | Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like
100 | d2hf1a1 |
| not modelled | 38.3 | 22 | Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like
101 | d1nuia2 |
| not modelled | 37.4 | 30 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:DNA primase zinc finger
102 | c2qkdA_ |
| not modelled | 37.1 | 16 | PDB header:signaling protein, cell cycle Chain: A: PDB Molecule:zinc finger protein zpr1; PDBTitle: crystal structure of tandem zpr1 domains
103 | c2yrcA_ |
| not modelled | 36.8 | 24 | PDB header:protein transport Chain: A: PDB Molecule:protein transport protein sec23a; PDBTitle: solution structure of the zf-sec23_sec24 from human sec23a
104 | d1lkoa2 |
| not modelled | 36.3 | 41 | Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Rubredoxin
105 | d1vd4a_ |
| not modelled | 36.1 | 33 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
106 | c2hl7A_ |
| not modelled | 35.8 | 67 | PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa
107 | c2d56A_ |
| not modelled | 34.5 | 26 | PDB header:antibiotic Chain: A: PDB Molecule:asabf; PDBTitle: solution structure of asabf, antibacterial peptide isolated2 from a nematode, ascaris suum
108 | d2qtva5 |
| not modelled | 34.3 | 23 | Fold:Rubredoxin-like Superfamily:Zn-finger domain of Sec23/24 Family:Zn-finger domain of Sec23/24
109 | c3zvzB_ |
| not modelled | 33.9 | 38 | PDB header:ligase Chain: B: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: phd finger of human uhrf1
110 | c3a44D_ |
| not modelled | 32.7 | 23 | PDB header:metal binding protein Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa; PDBTitle: crystal structure of hypa in the dimeric form
111 | c1pqvS_ |
| not modelled | 30.6 | 19 | PDB header:transferase/transcription Chain: S: PDB Molecule:transcription elongation factor s-ii; PDBTitle: rna polymerase ii-tfiis complex
112 | c1y1yS_ |
| not modelled | 30.6 | 22 | PDB header:transferase/transcription/dna-rna hybrid Chain: S: PDB Molecule:transcription elongation factor s-ii; PDBTitle: rna polymerase ii-tfiis-dna/rna complex
113 | c2qneA_ |
| not modelled | 30.2 | 18 | PDB header:transferase Chain: A: PDB Molecule:putative methyltransferase; PDBTitle: crystal structure of putative methyltransferase (zp_00558420.1) from2 desulfitobacterium hafniense y51 at 2.30 a resolution
114 | c2nn6I_ |
| not modelled | 30.1 | 23 | PDB header:hydrolase/transferase Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
115 | d2ct1a1 |
| not modelled | 29.9 | 38 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
116 | c2yg8B_ |
| not modelled | 29.3 | 19 | PDB header:hydrolase Chain: B: PDB Molecule:dna-3-methyladenine glycosidase ii, putative; PDBTitle: structure of an unusual 3-methyladenine dna glycosylase ii (2 alka) from deinococcus radiodurans
117 | c2o10A_ |
| not modelled | 29.1 | 24 | PDB header:metal binding protein Chain: A: PDB Molecule:muscle lim protein; PDBTitle: solution structure of the n-terminal lim domain of mlp/crp3
118 | c2kw0A_ |
| not modelled | 29.1 | 67 | PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli
119 | c2k5rA_ |
| not modelled | 28.9 | 12 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein xf2673; PDBTitle: solution nmr structure of xf2673 from xylella fastidiosa.2 northeast structural genomics consortium target xfr39
120 | c1x6aA_ |
| not modelled | 28.7 | 20 | PDB header:protein binding Chain: A: PDB Molecule:lim domain kinase 2; PDBTitle: solution structures of the second lim domain of human lim-2 kinase 2 (limk2)

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