Phyre 2 Results for P0CE52

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Email | l.a.kelley@imperial.ac.uk
Description | P0CE52
Date | Thu Jan 5 11:30:20 GMT 2012
Unique Job ID | 08704bce25c266ce

Summary |

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

Model (left) based on template d1musa_
Top template information
Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase)
Confidence and coverage
Confidence: | 98.2% | Coverage: | 55%
187 residues ( 55% of your sequence) have been modelled with 98.2% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | F | V | I | W | S | H | R | T | G | F | I | M | S | H | Q | L | T | F | A | D | S | E | F | S | S | K | R | R | Q | T | R | K | E | I | F | L | S | R | M | E | Q | I | L | P | W | Q | N | M | V | E | V | I | E | P | F | Y | P | K | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  | ? | ? | ? |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | G | N | G | R | R | P | Y | P | L | E | T | M | L | R | I | H | C | M | Q | H | W | Y | N | L | S | D | G | A | M | E | D | A | L | Y | E | I | A | S | M | R | L | F | A | R | L | S | L | D | S | A | L | P | D | R | T | T | I | M | N | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | R | H | L | L | E | Q | H | Q | L | A | R | Q | L | F | K | T | I | N | R | W | L | A | E | A | G | V | M | M | T | Q | G | T | L | V | D | A | T | I | I | E | A | P | S | S | T | K | N | K | E | Q | Q | R | D | P | E | M | H | Q | T | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | K | G | N | Q | W | H | F | G | M | K | A | H | I | G | V | D | A | K | S | G | L | T | H | S | L | V | T | T | A | A | N | E | H | D | L | N | Q | L | G | N | L | L | H | G | E | E | Q | F | V | S | A | D | A | G | Y | Q | G | A | P | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | R | E | E | L | A | E | V | D | V | D | W | L | I | A | E | R | P | G | K | V | R | T | L | K | Q | H | P | R | K | N | K | T | A | I | N | I | E | Y | M | K | A | S | I | R | A | R | V | E | H | P | F | R | I | I | K | R | Q | F | G | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | .
Sequence |  | V | K | A | R | Y | K | G | L | L | K | N | D | N | Q | L | A | M | L | F | T | L | A | N | L | F | R | A | D | Q | M | I | R | Q | W | E | R | S | 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 |
| d1musa_ |

### PDB 1mus chain A

Region: 123 - 321
Aligned: 187
Modelled: 198
Confidence: 98.2%
Identity: 12%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Transposase inhibitor (Tn5 transposase)

Phyre2
2 |
| d1b7ea_ |

### PDB 1b7e chain A

Region: 187 - 332
Aligned: 145
Modelled: 146
Confidence: 97.5%
Identity: 13%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Transposase inhibitor (Tn5 transposase)

Phyre2
3 |
| d1cxqa_ |

### PDB 1cxq chain A

Region: 144 - 323
Aligned: 130
Modelled: 131
Confidence: 84.2%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
4 |
| c3hefB_ |

### PDB 3hef chain B

Region: 87 - 212
Aligned: 115
Modelled: 126
Confidence: 79.7%
Identity: 14%
PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit

Phyre2
5 |
| d1asua_ |

### PDB 1asu chain A

Region: 191 - 323
Aligned: 108
Modelled: 111
Confidence: 70.0%
Identity: 20%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
6 |
| c3nf9A_ |

### PDB 3nf9 chain A

Region: 188 - 323
Aligned: 111
Modelled: 114
Confidence: 47.7%
Identity: 14%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design

Phyre2
7 |
| d1a9xa1 |

### PDB 1a9x chain A domain 1

Region: 36 - 98
Aligned: 50
Modelled: 63
Confidence: 39.7%
Identity: 16%
Fold: Carbamoyl phosphate synthetase, large subunit connection domain
Superfamily: Carbamoyl phosphate synthetase, large subunit connection domain
Family: Carbamoyl phosphate synthetase, large subunit connection domain

Phyre2
8 |
| d1c0ma2 |

### PDB 1c0m chain A domain 2

Region: 191 - 323
Aligned: 111
Modelled: 111
Confidence: 35.3%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
9 |
| c1c0mA_ |

### PDB 1c0m chain A

Region: 191 - 296
Aligned: 84
Modelled: 84
Confidence: 30.6%
Identity: 19%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2
10 |
| d1slma1 |

### PDB 1slm chain A domain 1

Region: 77 - 117
Aligned: 37
Modelled: 41
Confidence: 29.6%
Identity: 27%
Fold: PGBD-like
Superfamily: PGBD-like
Family: MMP N-terminal domain

Phyre2
11 |
| c3ohwB_ |

### PDB 3ohw chain B

Region: 63 - 112
Aligned: 45
Modelled: 50
Confidence: 22.4%
Identity: 16%
PDB header:protein binding
Chain: B: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide;
PDBTitle: x-ray structure of phycobilisome lcm core-membrane linker polypeptide2 (fragment 721-860) from synechocystis sp. pcc 6803, northeast3 structural genomics consortium target sgr209e

Phyre2
12 |
| c2ky4A_ |

### PDB 2ky4 chain A

Region: 63 - 112
Aligned: 45
Modelled: 50
Confidence: 22.4%
Identity: 16%
PDB header:photosynthesis
Chain: A: PDB Molecule:phycobilisome linker polypeptide;
PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome2 linker polypeptide from anabaena sp. northeast structural genomics3 consortium target nsr123e

Phyre2
13 |
| c2l3wA_ |

### PDB 2l3w chain A

Region: 63 - 112
Aligned: 45
Modelled: 50
Confidence: 20.8%
Identity: 20%
PDB header:photosynthesis
Chain: A: PDB Molecule:phycobilisome rod linker polypeptide;
PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome rod2 linker polypeptide from synechococcus elongatus, northeast structural3 genomics consortium target snr168a

Phyre2
14 |
| d1k78a1 |

### PDB 1k78 chain A domain 1

Region: 62 - 128
Aligned: 48
Modelled: 50
Confidence: 19.8%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
15 |
| c3pruD_ |

### PDB 3pru chain D

Region: 63 - 112
Aligned: 45
Modelled: 50
Confidence: 19.4%
Identity: 13%
PDB header:photosynthesis
Chain: D: PDB Molecule:phycobilisome 32.1 kda linker polypeptide, phycocyanin-
PDBTitle: crystal structure of phycobilisome 32.1 kda linker polypeptide,2 phycocyanin-associated, rod 1 (fragment 14-158) from synechocystis3 sp. pcc 6803, northeast structural genomics consortium target sgr182a

Phyre2
16 |
| c2l06A_ |

### PDB 2l06 chain A

Region: 63 - 112
Aligned: 45
Modelled: 50
Confidence: 18.7%
Identity: 22%
PDB header:protein binding
Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide;
PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c

Phyre2
17 |
| d1hyva_ |

### PDB 1hyv chain A

Region: 191 - 326
Aligned: 103
Modelled: 107
Confidence: 18.2%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
18 |
| c1q2iA_ |

### PDB 1q2i chain A

Region: 16 - 40
Aligned: 25
Modelled: 25
Confidence: 17.8%
Identity: 28%
PDB header:antitumor protein
Chain: A: PDB Molecule:pnc27;
PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells

Phyre2
19 |
| d1exqa_ |

### PDB 1exq chain A

Region: 193 - 323
Aligned: 99
Modelled: 102
Confidence: 16.0%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
20 |
| c3pvpA_ |

### PDB 3pvp chain A

Region: 44 - 143
Aligned: 83
Modelled: 83
Confidence: 15.9%
Identity: 14%
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1musa_ |
|  | 98.2 | 12 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase)
2 | d1b7ea_ |
|  | 97.5 | 13 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase)
3 | d1cxqa_ |
|  | 84.2 | 22 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
4 | c3hefB_ |
|  | 79.7 | 14 | PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
5 | d1asua_ |
|  | 70.0 | 20 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
6 | c3nf9A_ |
|  | 47.7 | 14 | PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
7 | d1a9xa1 |
|  | 39.7 | 16 | Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain
8 | d1c0ma2 |
|  | 35.3 | 15 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
9 | c1c0mA_ |
|  | 30.6 | 19 | PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase
10 | d1slma1 |
|  | 29.6 | 27 | Fold:PGBD-like Superfamily:PGBD-like Family:MMP N-terminal domain
11 | c3ohwB_ |
|  | 22.4 | 16 | PDB header:protein binding Chain: B: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: x-ray structure of phycobilisome lcm core-membrane linker polypeptide2 (fragment 721-860) from synechocystis sp. pcc 6803, northeast3 structural genomics consortium target sgr209e
12 | c2ky4A_ |
|  | 22.4 | 16 | PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome2 linker polypeptide from anabaena sp. northeast structural genomics3 consortium target nsr123e
13 | c2l3wA_ |
|  | 20.8 | 20 | PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome rod linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome rod2 linker polypeptide from synechococcus elongatus, northeast structural3 genomics consortium target snr168a
14 | d1k78a1 |
|  | 19.8 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
15 | c3pruD_ |
|  | 19.4 | 13 | PDB header:photosynthesis Chain: D: PDB Molecule:phycobilisome 32.1 kda linker polypeptide, phycocyanin- PDBTitle: crystal structure of phycobilisome 32.1 kda linker polypeptide,2 phycocyanin-associated, rod 1 (fragment 14-158) from synechocystis3 sp. pcc 6803, northeast structural genomics consortium target sgr182a
16 | c2l06A_ |
|  | 18.7 | 22 | PDB header:protein binding Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c
17 | d1hyva_ |
|  | 18.2 | 16 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
18 | c1q2iA_ |
|  | 17.8 | 28 | PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells
19 | d1exqa_ |
|  | 16.0 | 17 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
20 | c3pvpA_ |
|  | 15.9 | 14 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna
21 | c3f9kV_ |
| not modelled | 15.1 | 14 | PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
22 | d1su3a1 |
| not modelled | 14.8 | 28 | Fold:PGBD-like Superfamily:PGBD-like Family:MMP N-terminal domain
23 | c2o8kA_ |
| not modelled | 14.2 | 27 | PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element
24 | c3u1nC_ |
| not modelled | 14.2 | 12 | PDB header:hydrolase Chain: C: PDB Molecule:sam domain and hd domain-containing protein 1; PDBTitle: structure of the catalytic core of human samhd1
25 | c1k6yB_ |
| not modelled | 12.7 | 19 | PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
26 | c1x6iB_ |
| not modelled | 12.2 | 13 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ygfy; PDBTitle: crystal structure of ygfy from escherichia coli
27 | c1bg1A_ |
| not modelled | 10.9 | 11 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (transcription factor stat3b); PDBTitle: transcription factor stat3b/dna complex
28 | d2fug11 |
| not modelled | 9.9 | 19 | Fold:Bromodomain-like Superfamily:Nqo1C-terminal domain-like Family:Nqo1C-terminal domain-like
29 | d1nkua_ |
| not modelled | 9.1 | 13 | Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag)
30 | d2d1ha1 |
| not modelled | 8.3 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
31 | c3iwfA_ |
| not modelled | 8.3 | 4 | PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
32 | c2kvcA_ |
| not modelled | 8.2 | 20 | PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: solution structure of the mycobacterium tuberculosis protein rv0543c,2 a member of the duf3349 superfamily. seattle structural genomics3 center for infectious disease target mytud.17112.a
33 | d1sfka_ |
| not modelled | 7.6 | 19 | Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C
34 | d1s1ma2 |
| not modelled | 7.4 | 24 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
35 | d1c6va_ |
| not modelled | 7.3 | 14 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
36 | d1vcoa2 |
| not modelled | 6.8 | 18 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
37 | d1r6ra_ |
| not modelled | 5.9 | 10 | Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C
38 | c1r6rA_ |
| not modelled | 5.9 | 10 | PDB header:viral protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of dengue virus capsid protein reveals a2 new fold
39 | c1yvlB_ |
| not modelled | 5.7 | 9 | PDB header:signaling protein Chain: B: PDB Molecule:signal transducer and activator of transcription PDBTitle: structure of unphosphorylated stat1
40 | c1ud0B_ |
| not modelled | 5.6 | 20 | PDB header:chaperone Chain: B: PDB Molecule:70 kda heat-shock-like protein; PDBTitle: crystal structure of the c-terminal 10-kda subdomain of hsc70
41 | d1h3fa1 |
| not modelled | 5.6 | 9 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
42 | c2vkpA_ |
| not modelled | 5.6 | 12 | PDB header:protein-binding Chain: A: PDB Molecule:btb/poz domain-containing protein 6; PDBTitle: crystal structure of btb domain from btbd6
43 | c3d3kD_ |
| not modelled | 5.4 | 12 | PDB header:protein binding Chain: D: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p
44 | c1m6vE_ |
| not modelled | 5.4 | 16 | PDB header:ligase Chain: E: PDB Molecule:carbamoyl phosphate synthetase large chain; PDBTitle: crystal structure of the g359f (small subunit) point mutant of2 carbamoyl phosphate synthetase
45 | d1j1va_ |
| not modelled | 5.3 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Chromosomal replication initiation factor DnaA C-terminal domain IV
46 | c2lkyA_ |
| not modelled | 5.2 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of msmeg_1053, the second duf3349 annotated protein2 in the genome of mycobacterium smegmatis, seattle structural genomics3 center for infectious disease target mysma.17112.b

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