Phyre 2 Results for P09996

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Email | l.a.kelley@imperial.ac.uk
Description | P09996
Date | Thu Jan 5 11:02:37 GMT 2012
Unique Job ID | d80d58f98a062338

Summary |

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

Model (left) based on template d1z67a1
Top template information
Fold:YidB-like Superfamily:YidB-like Family:YidB-like
Confidence and coverage
Confidence: | 100.0% | Coverage: | 96%
127 residues ( 96% 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 | G | L | F | D | E | V | V | G | A | F | L | K | G | D | A | G | K | Y | Q | A | I | L | S | W | V | E | E | Q | G | G | I | Q | V | L | L | E | K | L | Q | S | G | G | L | G | A | I | L | S | T | W | L | S | N | Q | Q | G | N | Q | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  | ? |  | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | V | S | G | E | Q | L | E | S | A | L | G | T | N | A | V | S | D | L | G | Q | K | L | G | V | D | T | S | T | A | S | S | L | L | A | E | Q | L | P | K | I | I | D | A | L | S | P | Q | G | E | V | S | P | Q | A | N | N | D | L | L | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | .
Sequence |  | A | G | M | E | L | L | K | G | K | L | F | R
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 |
| d1z67a1 |

### PDB 1z67 chain A domain 1

Region: 3 - 131
Aligned: 127
Modelled: 129
Confidence: 100.0%
Identity: 97%
Fold: YidB-like
Superfamily: YidB-like
Family: YidB-like

Phyre2
2 |
| d1b8za_ |

### PDB 1b8z chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 68.4%
Identity: 21%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
3 |
| d1huua_ |

### PDB 1huu chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 66.2%
Identity: 18%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
4 |
| c2lfcA_ |

### PDB 2lfc chain A

Region: 73 - 96
Aligned: 24
Modelled: 24
Confidence: 62.9%
Identity: 4%
PDB header:oxidoreductase
Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit;
PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j

Phyre2
5 |
| d1y0pa3 |

### PDB 1y0p chain A domain 3

Region: 73 - 96
Aligned: 24
Modelled: 24
Confidence: 62.4%
Identity: 21%
Fold: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Phyre2
6 |
| d1d4ca3 |

### PDB 1d4c chain A domain 3

Region: 73 - 96
Aligned: 24
Modelled: 24
Confidence: 57.5%
Identity: 8%
Fold: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Phyre2
7 |
| c1tr8A_ |

### PDB 1tr8 chain A

Region: 70 - 95
Aligned: 26
Modelled: 26
Confidence: 57.3%
Identity: 15%
PDB header:chaperone
Chain: A: PDB Molecule:conserved protein (mth177);
PDBTitle: crystal structure of archaeal nascent polypeptide-associated complex2 (aenac)

Phyre2
8 |
| d1mula_ |

### PDB 1mul chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 53.3%
Identity: 21%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
9 |
| d1p71a_ |

### PDB 1p71 chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 51.6%
Identity: 28%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
10 |
| c3c4iA_ |

### PDB 3c4i chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 49.5%
Identity: 26%
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding protein hu homolog;
PDBTitle: crystal structure analysis of n terminal region containing the2 dimerization domain and dna binding domain of hu protein(histone like3 protein-dna binding) from mycobacterium tuberculosis [h37rv]

Phyre2
11 |
| d1qo8a3 |

### PDB 1qo8 chain A domain 3

Region: 73 - 96
Aligned: 24
Modelled: 24
Confidence: 47.6%
Identity: 13%
Fold: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Phyre2
12 |
| d1tafb_ |

### PDB 1taf chain B

Region: 68 - 95
Aligned: 28
Modelled: 28
Confidence: 47.3%
Identity: 25%
Fold: Histone-fold
Superfamily: Histone-fold
Family: TBP-associated factors, TAFs

Phyre2
13 |
| d1owfa_ |

### PDB 1owf chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 43.0%
Identity: 26%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
14 |
| d1l0oc_ |

### PDB 1l0o chain C

Region: 64 - 93
Aligned: 30
Modelled: 30
Confidence: 41.6%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2
15 |
| c1l0oC_ |

### PDB 1l0o chain C

Region: 64 - 93
Aligned: 30
Modelled: 30
Confidence: 41.6%
Identity: 17%
PDB header:protein binding
Chain: C: PDB Molecule:sigma factor;
PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf

Phyre2
16 |
| d1exea_ |

### PDB 1exe chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 40.2%
Identity: 21%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
17 |
| d2o97b1 |

### PDB 2o97 chain B domain 1

Region: 72 - 110
Aligned: 38
Modelled: 39
Confidence: 40.1%
Identity: 11%
Fold: IHF-like DNA-binding proteins
Superfamily: IHF-like DNA-binding proteins
Family: Prokaryotic DNA-bending protein

Phyre2
18 |
| c3ebnD_ |

### PDB 3ebn chain D

Region: 73 - 97
Aligned: 25
Modelled: 25
Confidence: 37.5%
Identity: 20%
PDB header:hydrolase
Chain: D: PDB Molecule:replicase polyprotein 1ab;
PDBTitle: a special dimerization of sars-cov main protease c-terminal2 domain due to domain-swapping

Phyre2
19 |
| d1uxca_ |

### PDB 1uxc chain A

Region: 74 - 93
Aligned: 20
Modelled: 20
Confidence: 34.8%
Identity: 25%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2
20 |
| d2p7vb1 |

### PDB 2p7v chain B domain 1

Region: 74 - 100
Aligned: 27
Modelled: 27
Confidence: 34.6%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1z67a1 |
|  | 100.0 | 97 | Fold:YidB-like Superfamily:YidB-like Family:YidB-like
2 | d1b8za_ |
|  | 68.4 | 21 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
3 | d1huua_ |
|  | 66.2 | 18 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
4 | c2lfcA_ |
|  | 62.9 | 4 | PDB header:oxidoreductase Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit; PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j
5 | d1y0pa3 |
|  | 62.4 | 21 | Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
6 | d1d4ca3 |
|  | 57.5 | 8 | Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
7 | c1tr8A_ |
|  | 57.3 | 15 | PDB header:chaperone Chain: A: PDB Molecule:conserved protein (mth177); PDBTitle: crystal structure of archaeal nascent polypeptide-associated complex2 (aenac)
8 | d1mula_ |
|  | 53.3 | 21 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
9 | d1p71a_ |
|  | 51.6 | 28 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
10 | c3c4iA_ |
|  | 49.5 | 26 | PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein hu homolog; PDBTitle: crystal structure analysis of n terminal region containing the2 dimerization domain and dna binding domain of hu protein(histone like3 protein-dna binding) from mycobacterium tuberculosis [h37rv]
11 | d1qo8a3 |
|  | 47.6 | 13 | Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
12 | d1tafb_ |
|  | 47.3 | 25 | Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs
13 | d1owfa_ |
|  | 43.0 | 26 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
14 | d1l0oc_ |
|  | 41.6 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
15 | c1l0oC_ |
|  | 41.6 | 17 | PDB header:protein binding Chain: C: PDB Molecule:sigma factor; PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf
16 | d1exea_ |
|  | 40.2 | 21 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
17 | d2o97b1 |
|  | 40.1 | 11 | Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein
18 | c3ebnD_ |
|  | 37.5 | 20 | PDB header:hydrolase Chain: D: PDB Molecule:replicase polyprotein 1ab; PDBTitle: a special dimerization of sars-cov main protease c-terminal2 domain due to domain-swapping
19 | d1uxca_ |
|  | 34.8 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
20 | d2p7vb1 |
|  | 34.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
21 | d2hsga1 |
| not modelled | 33.6 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
22 | d2phcb1 |
| not modelled | 33.1 | 13 | Fold:Cyclophilin-like Superfamily:Cyclophilin-like Family:PH0987 C-terminal domain-like
23 | d1qpza1 |
| not modelled | 32.1 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
24 | d1lcda_ |
| not modelled | 32.1 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
25 | c2iifA_ |
| not modelled | 31.8 | 26 | PDB header:recombination/dna Chain: A: PDB Molecule:integration host factor; PDBTitle: single chain integration host factor mutant protein (scihf2-2 k45ae) in complex with dna
26 | d2duca1 |
| not modelled | 30.3 | 20 | Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold
27 | c2zp2B_ |
| not modelled | 30.2 | 4 | PDB header:transferase inhibitor Chain: B: PDB Molecule:kinase a inhibitor; PDBTitle: c-terminal domain of kipi from bacillus subtilis
28 | c2w7nA_ |
| not modelled | 30.0 | 18 | PDB header:transcription/dna Chain: A: PDB Molecule:trfb transcriptional repressor protein; PDBTitle: crystal structure of kora bound to operator dna: insight2 into repressor cooperation in rp4 gene regulation
29 | c2lcvA_ |
| not modelled | 28.4 | 35 | PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
30 | d2cg4a1 |
| not modelled | 26.8 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
31 | d1uxda_ |
| not modelled | 25.8 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
32 | d2bjca1 |
| not modelled | 25.8 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
33 | c2l8nA_ |
| not modelled | 23.9 | 35 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional repressor cytr; PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna
34 | d1i1ga1 |
| not modelled | 23.7 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
35 | c3h5tA_ |
| not modelled | 23.4 | 25 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, laci family; PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
36 | c1bdhA_ |
| not modelled | 22.5 | 25 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
37 | d1z6ra1 |
| not modelled | 21.9 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain
38 | d1ku7a_ |
| not modelled | 21.4 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
39 | d1efaa1 |
| not modelled | 21.1 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
40 | d2cyya1 |
| not modelled | 21.1 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
41 | d2fug21 |
| not modelled | 21.1 | 4 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:NQO2-like
42 | d1ku3a_ |
| not modelled | 19.7 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
43 | c3kjxD_ |
| not modelled | 19.1 | 30 | PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator, laci family; PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
44 | d1wh5a_ |
| not modelled | 19.0 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
45 | c1or7A_ |
| not modelled | 19.0 | 13 | PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea
46 | c2phcB_ |
| not modelled | 18.5 | 13 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein ph0987; PDBTitle: crystal structure of conserved uncharacterized protein ph0987 from2 pyrococcus horikoshii
47 | d1tw3a1 |
| not modelled | 17.7 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Plant O-methyltransferase, N-terminal domain
48 | c1zvvA_ |
| not modelled | 17.7 | 19 | PDB header:transcription/dna Chain: A: PDB Molecule:glucose-resistance amylase regulator; PDBTitle: crystal structure of a ccpa-crh-dna complex
49 | d1ttya_ |
| not modelled | 17.4 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
50 | d1qzza1 |
| not modelled | 17.3 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Plant O-methyltransferase, N-terminal domain
51 | d3proc1 |
| not modelled | 17.2 | 13 | Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain
52 | d1x2na1 |
| not modelled | 16.8 | 0 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
53 | d2gqba1 |
| not modelled | 16.7 | 20 | Fold:RPA2825-like Superfamily:RPA2825-like Family:RPA2825-like
54 | d3e11a1 |
| not modelled | 16.7 | 11 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:TTHA0227-like
55 | d1wi9a_ |
| not modelled | 16.5 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PCI domain (PINT motif)
56 | d2cfxa1 |
| not modelled | 16.4 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
57 | c2da4A_ |
| not modelled | 15.6 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dkfzp686k21156; PDBTitle: solution structure of the homeobox domain of the2 hypothetical protein, dkfzp686k21156
58 | d1e3oc1 |
| not modelled | 15.5 | 6 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
59 | c3d23A_ |
| not modelled | 15.4 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:3c-like proteinase; PDBTitle: main protease of hcov-hku1
60 | d1x2ma1 |
| not modelled | 15.0 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
61 | d1or7a1 |
| not modelled | 15.0 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
62 | c2kz3A_ |
| not modelled | 14.5 | 19 | PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein rad51l3; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for human rad51d2 from 1 to 83
63 | c2cg4B_ |
| not modelled | 14.3 | 17 | PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc
64 | c3majA_ |
| not modelled | 14.3 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:dna processing chain a; PDBTitle: crystal structure of putative dna processing protein dpra from2 rhodopseudomonas palustris cga009
65 | c2q6fB_ |
| not modelled | 14.2 | 19 | PDB header:hydrolase Chain: B: PDB Molecule:infectious bronchitis virus (ibv) main protease; PDBTitle: crystal structure of infectious bronchitis virus (ibv) main2 protease in complex with a michael acceptor inhibitor n3
66 | c1rr7A_ |
| not modelled | 14.1 | 18 | PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu
67 | d1rr7a_ |
| not modelled | 14.1 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor
68 | d1alna1 |
| not modelled | 14.0 | 29 | Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase
69 | c1y66D_ |
| not modelled | 13.8 | 17 | PDB header:de novo protein Chain: D: PDB Molecule:engrailed homeodomain; PDBTitle: dioxane contributes to the altered conformation and2 oligomerization state of a designed engrailed homeodomain3 variant
70 | c2l4aA_ |
| not modelled | 13.8 | 10 | PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp
71 | d1e0ga_ |
| not modelled | 13.6 | 15 | Fold:LysM domain Superfamily:LysM domain Family:LysM domain
72 | d1bw5a_ |
| not modelled | 13.5 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
73 | d2cqxa1 |
| not modelled | 13.4 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
74 | c2yskA_ |
| not modelled | 13.4 | 22 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha1432; PDBTitle: crystal structure of a hypothetical protein ttha1432 from thermus2 thermophilus
75 | c2np2B_ |
| not modelled | 13.3 | 10 | PDB header:dna binding protein/dna Chain: B: PDB Molecule:hbb; PDBTitle: hbb-dna complex
76 | c2qufB_ |
| not modelled | 13.2 | 16 | PDB header:transcription Chain: B: PDB Molecule:transcription factor pf0095; PDBTitle: crystal structure of transcription factor axxa-pf0095 from pyrococcus2 furiosus
77 | d1p9sa_ |
| not modelled | 13.2 | 27 | Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold
78 | c3mmlD_ |
| not modelled | 13.0 | 4 | PDB header:hydrolase Chain: D: PDB Molecule:allophanate hydrolase subunit 1; PDBTitle: allophanate hydrolase complex from mycobacterium smegmatis, msmeg0435-2 msmeg0436
79 | d2ozua1 |
| not modelled | 12.8 | 15 | Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-acetyl transferase, NAT
80 | c1alnA_ |
| not modelled | 12.7 | 25 | PDB header:hydrolase Chain: A: PDB Molecule:cytidine deaminase; PDBTitle: crystal structure of cytidine deaminase complexed with 3-deazacytidine
81 | c2l0kA_ |
| not modelled | 12.5 | 37 | PDB header:transcription Chain: A: PDB Molecule:stage iii sporulation protein d; PDBTitle: nmr solution structure of a transcription factor spoiiid in complex2 with dna
82 | c2e1cA_ |
| not modelled | 12.5 | 14 | PDB header:transcription/dna Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519; PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
83 | c3t72o_ |
| not modelled | 12.5 | 19 | PDB header:transcription/dna Chain: O: PDB Molecule:pho box dna (strand 1); PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex
84 | c2da5A_ |
| not modelled | 12.4 | 6 | PDB header:dna binding protein Chain: A: PDB Molecule:zinc fingers and homeoboxes protein 3; PDBTitle: solution structure of the second homeobox domain of zinc2 fingers and homeoboxes protein 3 (triple homeobox 13 protein)
85 | d1mh3a1 |
| not modelled | 12.4 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
86 | c2djpA_ |
| not modelled | 12.3 | 20 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein sb145; PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145
87 | d1s7ea1 |
| not modelled | 12.2 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
88 | d2r5yb1 |
| not modelled | 12.2 | 28 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
89 | c4proD_ |
| not modelled | 12.0 | 12 | PDB header:serine protease Chain: D: PDB Molecule:alpha-lytic protease; PDBTitle: alpha-lytic protease complexed with pro region
90 | c2da7A_ |
| not modelled | 11.9 | 6 | PDB header:dna binding protein Chain: A: PDB Molecule:zinc finger homeobox protein 1b; PDBTitle: solution structure of the homeobox domain of zinc finger2 homeobox protein 1b (smad interacting protein 1)
91 | c3nauA_ |
| not modelled | 11.8 | 22 | PDB header:transcription Chain: A: PDB Molecule:zinc fingers and homeoboxes protein 2; PDBTitle: crystal structure of zhx2 hd2 (zinc-fingers and homeoboxes protein 2,2 homeodomain 2)
92 | c3f6wE_ |
| not modelled | 11.7 | 24 | PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000
93 | d1k61a_ |
| not modelled | 11.6 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
94 | c2a6eF_ |
| not modelled | 11.6 | 20 | PDB header:transferase Chain: F: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
95 | d2ecba1 |
| not modelled | 11.5 | 5 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
96 | d2hddb_ |
| not modelled | 11.5 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
97 | d1du6a_ |
| not modelled | 11.5 | 28 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
98 | d1j5ya1 |
| not modelled | 11.5 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
99 | c2k5eA_ |
| not modelled | 11.4 | 7 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of putative uncharacterized protein2 gsu1278 from methanocaldococcus jannaschii, northeast3 structural genomics consortium (nesg) target gsr195

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