Phyre 2 Results for P76062

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Email | l.a.kelley@imperial.ac.uk
Description | P76062
Date | Thu Jan 5 12:18:01 GMT 2012
Unique Job ID | 8eb80402d4271792

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3bd1B_
Top template information
PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1
Confidence and coverage
Confidence: | 96.5% | Coverage: | 34%
54 residues ( 34% of your sequence) have been modelled with 96.5% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
107 residues ( 68%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | L | S | G | K | D | L | G | R | A | I | E | Q | A | I | N | K | K | I | A | S | G | S | V | K | S | K | A | E | V | A | R | H | F | K | V | Q | P | P | S | I | Y | D | W | I | K | K | G | S | I | S | K | D | K | L | P | E | L | W | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | F | F | S | D | V | V | G | P | E | H | W | G | L | N | E | Y | P | I | P | T | P | T | N | S | D | T | K | S | E | L | L | D | I | N | N | L | Y | Q | A | A | S | D | E | I | R | A | I | V | A | F | L | L | S | G | N | A | T | E | P | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | .
Sequence |  | W | V | D | H | D | V | R | A | Y | I | A | A | M | E | M | K | V | G | K | Y | L | K | A | L | E | S | E | R | K | S | Q | N | I | T | K | T | G | T
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 |
| c3bd1B_ |

### PDB 3bd1 chain B

Region: 10 - 69
Aligned: 54
Modelled: 60
Confidence: 96.5%
Identity: 28%
PDB header:transcription
Chain: B: PDB Molecule:cro protein;
PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1

Phyre2
2 |
| c3bdnB_ |

### PDB 3bdn chain B

Region: 4 - 62
Aligned: 54
Modelled: 59
Confidence: 96.1%
Identity: 13%
PDB header:transcription/dna
Chain: B: PDB Molecule:lambda repressor;
PDBTitle: crystal structure of the lambda repressor

Phyre2
3 |
| c2fjrB_ |

### PDB 2fjr chain B

Region: 2 - 62
Aligned: 54
Modelled: 61
Confidence: 95.8%
Identity: 24%
PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186

Phyre2
4 |
| c2kpjA_ |

### PDB 2kpj chain A

Region: 3 - 80
Aligned: 73
Modelled: 78
Confidence: 95.1%
Identity: 22%
PDB header:transcription regulator
Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa;
PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a

Phyre2
5 |
| c3op9A_ |

### PDB 3op9 chain A

Region: 6 - 112
Aligned: 94
Modelled: 107
Confidence: 94.8%
Identity: 14%
PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua

Phyre2
6 |
| c3dnvB_ |

### PDB 3dnv chain B

Region: 1 - 62
Aligned: 57
Modelled: 62
Confidence: 93.9%
Identity: 11%
PDB header:transcription/dna
Chain: B: PDB Molecule:hth-type transcriptional regulator hipb;
PDBTitle: mdt protein

Phyre2
7 |
| d1r69a_ |

### PDB 1r69 chain A

Region: 7 - 62
Aligned: 51
Modelled: 56
Confidence: 93.7%
Identity: 18%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
8 |
| d1sq8a_ |

### PDB 1sq8 chain A

Region: 7 - 63
Aligned: 52
Modelled: 57
Confidence: 93.6%
Identity: 23%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
9 |
| c3clcC_ |

### PDB 3clc chain C

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 93.1%
Identity: 9%
PDB header:transcription regulator/dna
Chain: C: PDB Molecule:regulatory protein;
PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator

Phyre2
10 |
| d2croa_ |

### PDB 2cro chain A

Region: 7 - 62
Aligned: 51
Modelled: 56
Confidence: 93.0%
Identity: 16%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
11 |
| c3f52A_ |

### PDB 3f52 chain A

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 92.9%
Identity: 21%
PDB header:transcription activator
Chain: A: PDB Molecule:clp gene regulator (clgr);
PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum

Phyre2
12 |
| d1y9qa1 |

### PDB 1y9q chain A domain 1

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 92.9%
Identity: 9%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Probable transcriptional regulator VC1968, N-terminal domain

Phyre2
13 |
| d1llib_ |

### PDB 1lli chain B

Region: 4 - 62
Aligned: 54
Modelled: 59
Confidence: 92.9%
Identity: 13%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
14 |
| d1b0na2 |

### PDB 1b0n chain A domain 2

Region: 7 - 62
Aligned: 51
Modelled: 56
Confidence: 92.6%
Identity: 20%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2
15 |
| d2a6ca1 |

### PDB 2a6c chain A domain 1

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 92.4%
Identity: 15%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: NE1354

Phyre2
16 |
| c2ef8A_ |

### PDB 2ef8 chain A

Region: 7 - 67
Aligned: 56
Modelled: 61
Confidence: 92.0%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcription factor;
PDBTitle: crystal structure of c.ecot38is

Phyre2
17 |
| d2b5aa1 |

### PDB 2b5a chain A domain 1

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 91.7%
Identity: 19%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2
18 |
| d1adra_ |

### PDB 1adr chain A

Region: 7 - 63
Aligned: 52
Modelled: 57
Confidence: 91.7%
Identity: 17%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
19 |
| d1y7ya1 |

### PDB 1y7y chain A domain 1

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 91.6%
Identity: 11%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2
20 |
| c3ivpD_ |

### PDB 3ivp chain D

Region: 5 - 62
Aligned: 53
Modelled: 58
Confidence: 91.4%
Identity: 25%
PDB header:dna binding protein
Chain: D: PDB Molecule:putative transposon-related dna-binding protein;
PDBTitle: the structure of a possible transposon-related dna-binding protein2 from clostridium difficile 630.

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3bd1B_ |
|  | 96.5 | 28 | PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1
2 | c3bdnB_ |
|  | 96.1 | 13 | PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor
3 | c2fjrB_ |
|  | 95.8 | 24 | PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186
4 | c2kpjA_ |
|  | 95.1 | 22 | PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a
5 | c3op9A_ |
|  | 94.8 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua
6 | c3dnvB_ |
|  | 93.9 | 11 | PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein
7 | d1r69a_ |
|  | 93.7 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
8 | d1sq8a_ |
|  | 93.6 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
9 | c3clcC_ |
|  | 93.1 | 9 | PDB header:transcription regulator/dna Chain: C: PDB Molecule:regulatory protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator
10 | d2croa_ |
|  | 93.0 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
11 | c3f52A_ |
|  | 92.9 | 21 | PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
12 | d1y9qa1 |
|  | 92.9 | 9 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain
13 | d1llib_ |
|  | 92.9 | 13 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
14 | d1b0na2 |
|  | 92.6 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
15 | d2a6ca1 |
|  | 92.4 | 15 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
16 | c2ef8A_ |
|  | 92.0 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is
17 | d2b5aa1 |
|  | 91.7 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
18 | d1adra_ |
|  | 91.7 | 17 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
19 | d1y7ya1 |
|  | 91.6 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
20 | c3ivpD_ |
|  | 91.4 | 25 | PDB header:dna binding protein Chain: D: PDB Molecule:putative transposon-related dna-binding protein; PDBTitle: the structure of a possible transposon-related dna-binding protein2 from clostridium difficile 630.
21 | d1x57a1 |
| not modelled | 91.2 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like
22 | c2o38A_ |
| not modelled | 90.5 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator
23 | d2o38a1 |
| not modelled | 90.5 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
24 | d1lmb3_ |
| not modelled | 90.5 | 13 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
25 | c2elhA_ |
| not modelled | 90.3 | 30 | PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa
26 | c3cecA_ |
| not modelled | 90.0 | 22 | PDB header:transcription Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system; PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
27 | d1rzsa_ |
| not modelled | 89.8 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
28 | c2ewtA_ |
| not modelled | 89.3 | 17 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd
29 | d2r1jl1 |
| not modelled | 89.2 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
30 | c3b7hA_ |
| not modelled | 89.2 | 7 | PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11
31 | c3omtA_ |
| not modelled | 88.2 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
32 | c2xcjB_ |
| not modelled | 87.6 | 10 | PDB header:viral protein Chain: B: PDB Molecule:c protein; PDBTitle: crystal structure of p2 c, the immunity repressor of2 temperate e. coli phage p2
33 | c1b0nA_ |
| not modelled | 87.4 | 20 | PDB header:transcription regulator Chain: A: PDB Molecule:protein (sinr protein); PDBTitle: sinr protein/sini protein complex
34 | d1utxa_ |
| not modelled | 87.3 | 21 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
35 | d1bw6a_ |
| not modelled | 86.8 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
36 | c3f6wE_ |
| not modelled | 86.2 | 9 | 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
37 | c3eusB_ |
| not modelled | 86.2 | 9 | PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
38 | d2icta1 |
| not modelled | 86.0 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
39 | c3mlfC_ |
| not modelled | 85.3 | 19 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: putative transcriptional regulator from staphylococcus aureus.
40 | d1rioa_ |
| not modelled | 85.1 | 14 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
41 | c3bs3A_ |
| not modelled | 84.8 | 19 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis
42 | c1hlvA_ |
| not modelled | 83.9 | 24 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:major centromere autoantigen b; PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna
43 | c3t76A_ |
| not modelled | 82.9 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii
44 | d1hlva1 |
| not modelled | 82.6 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
45 | c3k2zA_ |
| not modelled | 81.9 | 24 | PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima
46 | c2jvlA_ |
| not modelled | 81.4 | 21 | PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
47 | d1g3wa1 |
| not modelled | 80.7 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
48 | d1j9ia_ |
| not modelled | 79.8 | 26 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain
49 | d2jn6a1 |
| not modelled | 79.8 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like
50 | d2isya1 |
| not modelled | 78.8 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
51 | c3fmyA_ |
| not modelled | 76.5 | 18 | PDB header:dna binding protein Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021)
52 | c3kxaD_ |
| not modelled | 76.2 | 19 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
53 | d2ev0a1 |
| not modelled | 76.2 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
54 | c1y9qA_ |
| not modelled | 74.1 | 11 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, hth_3 family; PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
55 | c3trbA_ |
| not modelled | 72.0 | 22 | PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii
56 | c2ppxA_ |
| not modelled | 70.5 | 10 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1735; PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens
57 | d2ppxa1 |
| not modelled | 70.5 | 10 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
58 | c3lisB_ |
| not modelled | 69.1 | 15 | PDB header:transcription Chain: B: PDB Molecule:csp231i c protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.csp231i (monoclinic form)
59 | c2wusR_ |
| not modelled | 68.8 | 9 | PDB header:structural protein Chain: R: PDB Molecule:putative uncharacterized protein; PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz
60 | c2ebyA_ |
| not modelled | 66.6 | 16 | PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli
61 | c2bnoA_ |
| not modelled | 65.4 | 11 | PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
62 | d2ofya1 |
| not modelled | 64.1 | 13 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
63 | c6paxA_ |
| not modelled | 61.4 | 19 | PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
64 | c1u78A_ |
| not modelled | 58.5 | 19 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
65 | d1pdnc_ |
| not modelled | 58.3 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
66 | c3fymA_ |
| not modelled | 58.1 | 11 | PDB header:dna binding protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the 1a structure of ymfm, a putative dna-binding membrane2 protein from staphylococcus aureus
67 | d3ctaa1 |
| not modelled | 57.9 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
68 | c2rn7A_ |
| not modelled | 55.6 | 14 | PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125
69 | c2hinA_ |
| not modelled | 54.9 | 32 | PDB header:transcription Chain: A: PDB Molecule:repressor protein; PDBTitle: structure of n15 cro at 1.05 a: an ortholog of lambda cro2 with a completely different but equally effective3 dimerization mechanism
70 | d1jhfa1 |
| not modelled | 54.7 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain
71 | c1f5tA_ |
| not modelled | 52.2 | 15 | PDB header:transcription/dna Chain: A: PDB Molecule:diphtheria toxin repressor; PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
72 | d2coba1 |
| not modelled | 51.9 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain
73 | c2h09A_ |
| not modelled | 51.5 | 17 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator mntr; PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
74 | c3gn5B_ |
| not modelled | 47.8 | 13 | 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)
75 | c1g3wA_ |
| not modelled | 45.3 | 14 | PDB header:gene regulation Chain: A: PDB Molecule:diphtheria toxin repressor; PDBTitle: cd-cys102ser dtxr
76 | d1d1la_ |
| not modelled | 44.2 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
77 | d2cg4a1 |
| not modelled | 43.8 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
78 | d6paxa1 |
| not modelled | 43.5 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
79 | d2cfxa1 |
| not modelled | 42.1 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
80 | c3ctaA_ |
| not modelled | 41.7 | 19 | PDB header:transferase Chain: A: PDB Molecule:riboflavin kinase; PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
81 | d1zs4a1 |
| not modelled | 38.3 | 26 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Bacteriophage CII protein
82 | d4croa_ |
| not modelled | 37.4 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
83 | d1nera_ |
| not modelled | 37.1 | 15 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
84 | c2x4hA_ |
| not modelled | 36.4 | 20 | PDB header:transcription Chain: A: PDB Molecule:hypothetical protein sso2273; PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
85 | c2pijB_ |
| not modelled | 36.3 | 17 | PDB header:transcription Chain: B: PDB Molecule:prophage pfl 6 cro; PDBTitle: structure of the cro protein from prophage pfl 6 in pseudomonas2 fluorescens pf-5
86 | c1fx7C_ |
| not modelled | 34.1 | 14 | PDB header:signaling protein Chain: C: PDB Molecule:iron-dependent repressor ider; PDBTitle: crystal structure of the iron-dependent regulator (ider)2 from mycobacterium tuberculosis
87 | d3orca_ |
| not modelled | 32.5 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
88 | c2ao9H_ |
| not modelled | 31.8 | 19 | PDB header:structural genomics, unknown function Chain: H: PDB Molecule:phage protein; PDBTitle: structural genomics, the crystal structure of a phage protein2 (phbc6a51) from bacillus cereus atcc 14579
89 | c2o8xA_ |
| not modelled | 31.7 | 16 | PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
90 | d1jkva_ |
| not modelled | 30.9 | 17 | Fold:Ferritin-like Superfamily:Ferritin-like Family:Manganese catalase (T-catalase)
91 | d1k78a1 |
| not modelled | 30.4 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
92 | d1vz0a1 |
| not modelled | 29.6 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like
93 | c2it0A_ |
| not modelled | 27.9 | 14 | PDB header:transcription/dna Chain: A: PDB Molecule:iron-dependent repressor ider; PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
94 | d1or7a1 |
| not modelled | 27.1 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
95 | d1xsva_ |
| not modelled | 27.0 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
96 | d1i1ga1 |
| not modelled | 26.7 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
97 | c3i4pA_ |
| not modelled | 26.1 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
98 | c3hefB_ |
| not modelled | 25.8 | 18 | PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
99 | c2l4aA_ |
| not modelled | 25.6 | 14 | 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
100 | c2ev5B_ |
| not modelled | 25.6 | 23 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator mntr; PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
101 | d1qnta2 |
| not modelled | 25.6 | 28 | Fold:Ribonuclease H-like motif Superfamily:Methylated DNA-protein cysteine methyltransferase domain Family:Methylated DNA-protein cysteine methyltransferase domain
102 | d1rp3a2 |
| not modelled | 25.0 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
103 | c2cg4B_ |
| not modelled | 24.7 | 24 | PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc
104 | d2cyya1 |
| not modelled | 24.2 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
105 | d2g7ga1 |
| not modelled | 23.5 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
106 | c3tgnA_ |
| not modelled | 22.5 | 26 | PDB header:transcription Chain: A: PDB Molecule:adc operon repressor adcr; PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state
107 | d1xrsb2 |
| not modelled | 22.3 | 35 | Fold:Dodecin subunit-like Superfamily:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Family:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain
108 | c2k27A_ |
| not modelled | 22.2 | 19 | PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain
109 | c3hugA_ |
| not modelled | 22.0 | 14 | PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
110 | c2vbzA_ |
| not modelled | 21.2 | 11 | PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan
111 | c3qsvD_ |
| not modelled | 20.8 | 11 | PDB header:transcription/dna Chain: D: PDB Molecule:mothers against decapentaplegic homolog 4; PDBTitle: structural basis for dna recognition by constitutive smad4 mh1 dimers
112 | c1z4hA_ |
| not modelled | 20.3 | 26 | PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:tor inhibition protein; PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase
113 | d2vkea1 |
| not modelled | 20.3 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
114 | d3broa1 |
| not modelled | 20.3 | 4 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators

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