Phyre 2 Results for P52133

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Email | l.a.kelley@imperial.ac.uk
Description | P52133
Date | Thu Jan 5 12:05:38 GMT 2012
Unique Job ID | dd655207642ded7a

Summary |

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

Model (left) based on template d1j5ya1
Top template information
Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
Confidence and coverage
Confidence: | 98.7% | Coverage: | 24%
56 residues ( 24% of your sequence) have been modelled with 98.7% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
108 residues ( 46%) 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 | T | Q | A | E | R | R | H | D | R | L | A | V | R | L | S | L | I | I | S | R | L | V | A | G | E | T | L | S | V | R | K | L | A | A | E | F | G | V | S | V | R | T | L | R | R | D | F | R | E | R | L | M | Y | L | D | L | E | Y | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | G | Y | C | R | L | R | T | A | G | S | E | M | Q | M | V | P | D | V | L | I | F | A | H | R | S | G | L | A | G | L | F | P | G | L | D | R | R | L | V | N | A | L | L | M | C | D | E | S | P | C | V | I | A | P | A | N | P | V | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | S | P | S | G | A | L | S | F | W | R | L | I | Q | A | I | T | G | R | R | R | V | T | L | I | A | E | G | R | R | C | E | R | L | A | P | C | R | L | L | I | H | Q | Q | T | W | Y | L | V | A | E | H | E | G | H | I | A | V | F | T | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | .
Sequence |  | D | E | I | H | L | I | Q | P | L | Q | E | T | F | R | R | N | D | S | L | C | R | L | V | E | D | P | V | F | I | Q | A | L | P | H | F | R | F | I | Q | H | S | L | L | T | F | V | P | A | D | S | P | P | E
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 |
| d1j5ya1 |

### PDB 1j5y chain A domain 1

Region: 14 - 69
Aligned: 56
Modelled: 56
Confidence: 98.7%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2
2 |
| d1biaa1 |

### PDB 1bia chain A domain 1

Region: 14 - 69
Aligned: 56
Modelled: 56
Confidence: 98.6%
Identity: 21%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2
3 |
| c1j5yA_ |

### PDB 1j5y chain A

Region: 14 - 69
Aligned: 56
Modelled: 56
Confidence: 98.4%
Identity: 21%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution

Phyre2
4 |
| d1aoya_ |

### PDB 1aoy chain A

Region: 1 - 73
Aligned: 69
Modelled: 73
Confidence: 96.5%
Identity: 10%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Arginine repressor (ArgR), N-terminal DNA-binding domain

Phyre2
5 |
| d1stza1 |

### PDB 1stz chain A domain 1

Region: 14 - 63
Aligned: 50
Modelled: 50
Confidence: 96.3%
Identity: 12%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Heat-inducible transcription repressor HrcA, N-terminal domain

Phyre2
6 |
| c2ewnA_ |

### PDB 2ewn chain A

Region: 16 - 69
Aligned: 54
Modelled: 54
Confidence: 96.3%
Identity: 22%
PDB header:ligase, transcription
Chain: A: PDB Molecule:bira bifunctional protein;
PDBTitle: ecoli biotin repressor with co-repressor analog

Phyre2
7 |
| d1mkma1 |

### PDB 1mkm chain A domain 1

Region: 12 - 67
Aligned: 56
Modelled: 56
Confidence: 95.9%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Transcriptional regulator IclR, N-terminal domain

Phyre2
8 |
| c3by6C_ |

### PDB 3by6 chain C

Region: 1 - 68
Aligned: 68
Modelled: 68
Confidence: 95.9%
Identity: 19%
PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni

Phyre2
9 |
| c2l4aA_ |

### PDB 2l4a chain A

Region: 1 - 59
Aligned: 59
Modelled: 59
Confidence: 95.8%
Identity: 17%
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

Phyre2
10 |
| d1b4aa1 |

### PDB 1b4a chain A domain 1

Region: 12 - 65
Aligned: 54
Modelled: 54
Confidence: 95.8%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Arginine repressor (ArgR), N-terminal DNA-binding domain

Phyre2
11 |
| c1b4aA_ |

### PDB 1b4a chain A

Region: 12 - 65
Aligned: 54
Modelled: 54
Confidence: 95.7%
Identity: 19%
PDB header:repressor
Chain: A: PDB Molecule:arginine repressor;
PDBTitle: structure of the arginine repressor from bacillus stearothermophilus

Phyre2
12 |
| d2p5ka1 |

### PDB 2p5k chain A domain 1

Region: 12 - 65
Aligned: 54
Modelled: 54
Confidence: 95.5%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Arginine repressor (ArgR), N-terminal DNA-binding domain

Phyre2
13 |
| c3eetA_ |

### PDB 3eet chain A

Region: 7 - 77
Aligned: 71
Modelled: 71
Confidence: 95.4%
Identity: 20%
PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator

Phyre2
14 |
| c3ereD_ |

### PDB 3ere chain D

Region: 12 - 92
Aligned: 81
Modelled: 81
Confidence: 95.4%
Identity: 21%
PDB header:dna binding protein/dna
Chain: D: PDB Molecule:arginine repressor;
PDBTitle: crystal structure of the arginine repressor protein from mycobacterium2 tuberculosis in complex with the dna operator

Phyre2
15 |
| d2cg4a1 |

### PDB 2cg4 chain A domain 1

Region: 16 - 51
Aligned: 36
Modelled: 36
Confidence: 95.4%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Lrp/AsnC-like transcriptional regulator N-terminal domain

Phyre2
16 |
| c2y75F_ |

### PDB 2y75 chain F

Region: 6 - 69
Aligned: 64
Modelled: 64
Confidence: 95.3%
Identity: 11%
PDB header:transcription
Chain: F: PDB Molecule:hth-type transcriptional regulator cymr;
PDBTitle: the structure of cymr (yrzc) the global cysteine regulator2 of b. subtilis

Phyre2
17 |
| c2g7uB_ |

### PDB 2g7u chain B

Region: 10 - 67
Aligned: 58
Modelled: 58
Confidence: 95.2%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: 2.3 a structure of putative catechol degradative operon regulator from2 rhodococcus sp. rha1

Phyre2
18 |
| c3lmmA_ |

### PDB 3lmm chain A

Region: 5 - 68
Aligned: 64
Modelled: 64
Confidence: 95.1%
Identity: 11%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35

Phyre2
19 |
| c1mkmA_ |

### PDB 1mkm chain A

Region: 12 - 67
Aligned: 56
Modelled: 56
Confidence: 95.1%
Identity: 14%
PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr

Phyre2
20 |
| d2hs5a1 |

### PDB 2hs5 chain A domain 1

Region: 6 - 70
Aligned: 65
Modelled: 65
Confidence: 95.0%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: GntR-like transcriptional regulators

Phyre2
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| c3c7jA_ |

### PDB 3c7j chain A

Region: 2 - 108
Aligned: 107
Modelled: 106
Confidence: 94.6%
Identity: 22%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of transcriptional regulator (gntr family member)2 from pseudomonas syringae pv. tomato str. dc3000

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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1j5ya1 |
|  | 98.7 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
2 | d1biaa1 |
|  | 98.6 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
3 | c1j5yA_ |
|  | 98.4 | 21 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family; PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
4 | d1aoya_ |
|  | 96.5 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
5 | d1stza1 |
|  | 96.3 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
6 | c2ewnA_ |
|  | 96.3 | 22 | PDB header:ligase, transcription Chain: A: PDB Molecule:bira bifunctional protein; PDBTitle: ecoli biotin repressor with co-repressor analog
7 | d1mkma1 |
|  | 95.9 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator IclR, N-terminal domain
8 | c3by6C_ |
|  | 95.9 | 19 | PDB header:transcription regulator Chain: C: PDB Molecule:predicted transcriptional regulator; PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
9 | c2l4aA_ |
|  | 95.8 | 17 | 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
10 | d1b4aa1 |
|  | 95.8 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
11 | c1b4aA_ |
|  | 95.7 | 19 | PDB header:repressor Chain: A: PDB Molecule:arginine repressor; PDBTitle: structure of the arginine repressor from bacillus stearothermophilus
12 | d2p5ka1 |
|  | 95.5 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
13 | c3eetA_ |
|  | 95.4 | 20 | PDB header:transcription regulator Chain: A: PDB Molecule:putative gntr-family transcriptional regulator; PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
14 | c3ereD_ |
|  | 95.4 | 21 | PDB header:dna binding protein/dna Chain: D: PDB Molecule:arginine repressor; PDBTitle: crystal structure of the arginine repressor protein from mycobacterium2 tuberculosis in complex with the dna operator
15 | d2cg4a1 |
|  | 95.4 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
16 | c2y75F_ |
|  | 95.3 | 11 | PDB header:transcription Chain: F: PDB Molecule:hth-type transcriptional regulator cymr; PDBTitle: the structure of cymr (yrzc) the global cysteine regulator2 of b. subtilis
17 | c2g7uB_ |
|  | 95.2 | 17 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: 2.3 a structure of putative catechol degradative operon regulator from2 rhodococcus sp. rha1
18 | c3lmmA_ |
|  | 95.1 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35
19 | c1mkmA_ |
|  | 95.1 | 14 | PDB header:transcription Chain: A: PDB Molecule:iclr transcriptional regulator; PDBTitle: crystal structure of the thermotoga maritima iclr
20 | d2hs5a1 |
|  | 95.0 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
21 | c2h09A_ |
| not modelled | 94.9 | 20 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator mntr; PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
22 | c2vbzA_ |
| not modelled | 94.9 | 22 | 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
23 | d1i1ga1 |
| not modelled | 94.8 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
24 | c1f5tA_ |
| not modelled | 94.7 | 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
25 | c2x4hA_ |
| not modelled | 94.7 | 9 | PDB header:transcription Chain: A: PDB Molecule:hypothetical protein sso2273; PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
26 | c3lwfD_ |
| not modelled | 94.7 | 14 | PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator (np_470886.1)2 from listeria innocua at 2.06 a resolution
27 | c3c7jA_ |
|  | 94.6 | 22 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of transcriptional regulator (gntr family member)2 from pseudomonas syringae pv. tomato str. dc3000
28 | c2xroE_ |
| not modelled | 94.6 | 22 | PDB header:dna-binding protein/dna Chain: E: PDB Molecule:hth-type transcriptional regulator ttgv; PDBTitle: crystal structure of ttgv in complex with its dna operator
29 | c1hlvA_ |
| not modelled | 94.6 | 23 | 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
30 | d1f9na1 |
| not modelled | 94.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
31 | d1u2wa1 |
| not modelled | 94.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
32 | d2cyya1 |
| not modelled | 94.5 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
33 | c3neuA_ |
| not modelled | 94.4 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin1836 protein; PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
34 | d2cfxa1 |
| not modelled | 94.3 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
35 | c2oqgA_ |
| not modelled | 94.2 | 15 | PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
36 | d2d1ha1 |
| not modelled | 94.2 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
37 | c2it0A_ |
| not modelled | 94.1 | 17 | 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
38 | c3f8mA_ |
| not modelled | 94.1 | 24 | PDB header:transcription Chain: A: PDB Molecule:gntr-family protein transcriptional regulator; PDBTitle: crystal structure of phnf from mycobacterium smegmatis
39 | c3cuoB_ |
| not modelled | 94.0 | 15 | PDB header:transcription regulator Chain: B: PDB Molecule:uncharacterized hth-type transcriptional regulator ygav; PDBTitle: crystal structure of the predicted dna-binding transcriptional2 regulator from e. coli
40 | d2dt5a1 |
| not modelled | 93.9 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional repressor Rex, N-terminal domain
41 | d1v4ra1 |
| not modelled | 93.9 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
42 | d3bwga1 |
| not modelled | 93.9 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
43 | c2cg4B_ |
| not modelled | 93.9 | 25 | PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc
44 | c2e1cA_ |
| not modelled | 93.8 | 18 | 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
45 | c3i4pA_ |
| not modelled | 93.8 | 23 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
46 | c2e7xA_ |
| not modelled | 93.7 | 19 | PDB header:transcription regulator Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator; PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand
47 | d1z05a1 |
| not modelled | 93.7 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain
48 | c2ia0A_ |
| not modelled | 93.7 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864; PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864)
49 | c2di3A_ |
| not modelled | 93.7 | 20 | PDB header:transcription Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family; PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
50 | c2du9A_ |
| not modelled | 93.7 | 15 | PDB header:transcription Chain: A: PDB Molecule:predicted transcriptional regulators; PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
51 | c3v4gA_ |
| not modelled | 93.6 | 8 | PDB header:dna binding protein Chain: A: PDB Molecule:arginine repressor; PDBTitle: 1.60 angstrom resolution crystal structure of an arginine repressor2 from vibrio vulnificus cmcp6
52 | c2jscB_ |
| not modelled | 93.6 | 17 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
53 | c2hs5A_ |
| not modelled | 93.5 | 26 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcriptional regulator gntr; PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator gntr from rhodococcus sp. rha1
54 | d1hw1a1 |
| not modelled | 93.5 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
55 | c3bwgA_ |
| not modelled | 93.5 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:uncharacterized hth-type transcriptional regulator yydk; PDBTitle: the crystal structure of possible transcriptional regulator yydk from2 bacillus subtilis subsp. subtilis str. 168
56 | c1i1gA_ |
| not modelled | 93.3 | 17 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
57 | c2p6tH_ |
| not modelled | 93.2 | 14 | PDB header:transcription Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family; PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis
58 | c2cfxD_ |
| not modelled | 93.0 | 25 | PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc
59 | d1r1ua_ |
| not modelled | 93.0 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
60 | c3ihuA_ |
| not modelled | 92.9 | 17 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of dna binding protein (yp_298823.1) from ralstonia2 eutropha jmp134 at 1.92 a resolution
61 | d1o57a1 |
| not modelled | 92.9 | 7 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:N-terminal domain of Bacillus PurR
62 | c1bl0A_ |
| not modelled | 92.9 | 25 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
63 | c2zkzC_ |
| not modelled | 92.8 | 11 | PDB header:transcription Chain: C: PDB Molecule:transcriptional repressor pagr; PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
64 | c1r22B_ |
| not modelled | 92.6 | 27 | PDB header:transcription repressor Chain: B: PDB Molecule:transcriptional repressor smtb; PDBTitle: crystal structure of the cyanobacterial metallothionein2 repressor smtb (c14s/c61s/c121s mutant) in the zn2alpha5-3 form
65 | c3r4kD_ |
| not modelled | 92.6 | 14 | PDB header:dna binding protein Chain: D: PDB Molecule:transcriptional regulator, iclr family; PDBTitle: crystal structure of a putative iclr transcriptional regulator2 (tm1040_3717) from silicibacter sp. tm1040 at 2.46 a resolution
66 | c2dbbA_ |
| not modelled | 92.6 | 17 | PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061
67 | c3edpB_ |
| not modelled | 92.5 | 16 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:lin2111 protein; PDBTitle: the crystal structure of the protein lin2111 (functionally unknown)2 from listeria innocua clip11262
68 | c2dt5A_ |
| not modelled | 92.4 | 21 | PDB header:dna binding protein Chain: A: PDB Molecule:at-rich dna-binding protein; PDBTitle: crystal structure of ttha1657 (at-rich dna-binding protein) from2 thermus thermophilus hb8
69 | c2o0yB_ |
| not modelled | 92.3 | 16 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator rha1_ro069532 (iclr-family) from rhodococcus sp.
70 | c3k69A_ |
| not modelled | 92.3 | 19 | PDB header:transcription Chain: A: PDB Molecule:putative transcription regulator; PDBTitle: crystal structure of a putative transcriptional regulator (lp_0360)2 from lactobacillus plantarum at 1.95 a resolution
71 | d1r1ta_ |
| not modelled | 92.3 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
72 | c1g3wA_ |
| not modelled | 92.3 | 15 | PDB header:gene regulation Chain: A: PDB Molecule:diphtheria toxin repressor; PDBTitle: cd-cys102ser dtxr
73 | d1g3wa1 |
| not modelled | 92.1 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
74 | c1zgwA_ |
| not modelled | 92.1 | 14 | PDB header:transcription regulator/dna Chain: A: PDB Molecule:ada polyprotein; PDBTitle: nmr structure of e. coli ada protein in complex with dna
75 | c3ketA_ |
| not modelled | 92.1 | 27 | PDB header:transcription/dna Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: crystal structure of a rex-family transcriptional regulatory protein2 from streptococcus agalactiae bound to a palindromic operator
76 | d1xd7a_ |
| not modelled | 92.1 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator Rrf2
77 | d1j9ia_ |
| not modelled | 92.1 | 25 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain
78 | c3f6oB_ |
| not modelled | 91.9 | 15 | PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
79 | d2p4wa1 |
| not modelled | 91.8 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF1790-like
80 | c2l0kA_ |
| not modelled | 91.7 | 41 | 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
81 | c2wteB_ |
| not modelled | 91.7 | 17 | PDB header:antiviral protein Chain: B: PDB Molecule:csa3; PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
82 | d2ev0a1 |
| not modelled | 91.6 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
83 | c3h5tA_ |
| not modelled | 91.5 | 20 | 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
84 | c2k9sA_ |
| not modelled | 91.5 | 19 | PDB header:transcription Chain: A: PDB Molecule:arabinose operon regulatory protein; PDBTitle: solution structure of dna binding domain of e. coli arac
85 | c3eqxB_ |
| not modelled | 91.5 | 5 | PDB header:dna binding protein Chain: B: PDB Molecule:fic domain containing transcriptional regulator; PDBTitle: crystal structure of a fic family protein (so_4266) from shewanella2 oneidensis at 1.6 a resolution
86 | d2isya1 |
| not modelled | 91.4 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
87 | d1y0ua_ |
| not modelled | 91.3 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
88 | c3pqkD_ |
| not modelled | 91.2 | 24 | PDB header:transcription Chain: D: PDB Molecule:biofilm growth-associated repressor; PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
89 | c3fmsA_ |
| not modelled | 91.0 | 20 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
90 | d1a04a1 |
| not modelled | 90.8 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
91 | c1fx7C_ |
| not modelled | 90.6 | 17 | 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
92 | d1hlva1 |
| not modelled | 90.5 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
93 | c2kpjA_ |
| not modelled | 90.5 | 20 | 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
94 | c3oioA_ |
| not modelled | 90.2 | 38 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain- PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum
95 | c3mq0A_ |
| not modelled | 90.2 | 12 | PDB header:transcription repressor Chain: A: PDB Molecule:transcriptional repressor of the blcabc operon; PDBTitle: crystal structure of agobacterium tumefaciens repressor blcr
96 | c2vt2A_ |
| not modelled | 90.1 | 33 | PDB header:transcription Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: structure and functional properties of the bacillus2 subtilis transcriptional repressor rex
97 | c1e2xA_ |
| not modelled | 90.1 | 19 | PDB header:transcriptional regulation Chain: A: PDB Molecule:fatty acid metabolism regulator protein; PDBTitle: fadr, fatty acid responsive transcription factor from e.2 coli
98 | c3jthA_ |
| not modelled | 90.0 | 27 | PDB header:transcription Chain: A: PDB Molecule:transcription activator hlyu; PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
99 | c2gqqB_ |
| not modelled | 89.9 | 19 | PDB header:transcription Chain: B: PDB Molecule:leucine-responsive regulatory protein; PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
100 | c1y9qA_ |
| not modelled | 89.9 | 22 | 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
101 | c3f6vA_ |
| not modelled | 89.8 | 22 | PDB header:transcription regulator Chain: A: PDB Molecule:possible transcriptional regulator, arsr family PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
102 | d1rioa_ |
| not modelled | 89.7 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
103 | c2ev5B_ |
| not modelled | 89.6 | 11 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator mntr; PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
104 | c3oouA_ |
| not modelled | 89.5 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua
105 | d1z6ra1 |
| not modelled | 89.4 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain
106 | d2ofya1 |
| not modelled | 89.2 | 29 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
107 | c3cjnA_ |
| not modelled | 89.1 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
108 | d1lmb3_ |
| not modelled | 88.9 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
109 | d1bl0a1 |
| not modelled | 88.9 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
110 | c2ppxA_ |
| not modelled | 88.9 | 21 | 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
111 | d2ppxa1 |
| not modelled | 88.9 | 21 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
112 | c1z6rC_ |
| not modelled | 88.9 | 11 | PDB header:transcription Chain: C: PDB Molecule:mlc protein; PDBTitle: crystal structure of mlc from escherichia coli
113 | d1llib_ |
| not modelled | 88.8 | 26 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
114 | c3kjxD_ |
| not modelled | 88.8 | 32 | 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
115 | d1ylfa1 |
| not modelled | 88.7 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator Rrf2
116 | c2ef8A_ |
| not modelled | 88.7 | 26 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is
117 | c3mn2B_ |
| not modelled | 88.7 | 21 | PDB header:transcription regulator Chain: B: PDB Molecule:probable arac family transcriptional regulator; PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
118 | c3fmyA_ |
| not modelled | 88.6 | 21 | 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)
119 | c1z05A_ |
| not modelled | 88.5 | 13 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, rok family; PDBTitle: crystal structure of the rok family transcriptional regulator, homolog2 of e.coli mlc protein.
120 | c2w48D_ |
| not modelled | 88.4 | 24 | PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae

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