Phyre 2 Results for P19768

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Email | l.a.kelley@imperial.ac.uk
Description | P19768
Date | Thu Jan 5 11:37:32 GMT 2012
Unique Job ID | 3a3fdf6e9ce65683

Summary |

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

Model (left) based on template d2jn6a1
Top template information
Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like
Confidence and coverage
Confidence: | 99.5% | Coverage: | 48%
83 residues ( 48% of your sequence) have been modelled with 99.5% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
145 residues ( 84%) 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 | S | K | P | K | Y | P | F | E | K | R | L | E | V | V | N | H | Y | F | T | T | D | D | G | Y | R | I | I | S | A | R | F | G | V | P | R | T | Q | V | R | T | W | V | A | L | Y | E | K | H | G | E | K | G | L | I | P | K | P | K | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  | ? |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | V | S | A | D | P | E | L | R | I | K | V | V | K | A | V | I | E | Q | H | M | S | L | N | Q | A | A | A | H | F | M | L | A | G | S | G | S | V | A | R | W | L | K | V | Y | E | E | R | G | E | A | G | L | R | A | L | K | I | G | T | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | .
Sequence |  | R | N | I | A | I | S | V | D | P | E | K | A | A | S | A | L | E | L | S | K | D | R | R | I | E | D | L | E | R | Q | V | R | F | L | E | T | R | L | M | Y | L | K | K | L | K | A | L | A | H | P | T | K | K
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 |
| d2jn6a1 |

### PDB 2jn6 chain A domain 1

Region: 59 - 161
Aligned: 83
Modelled: 84
Confidence: 99.5%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Cgl2762-like

Phyre2
2 |
| c2rn7A_ |

### PDB 2rn7 chain A

Region: 57 - 163
Aligned: 85
Modelled: 86
Confidence: 99.4%
Identity: 24%
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

Phyre2
3 |
| c1u78A_ |

### PDB 1u78 chain A

Region: 2 - 103
Aligned: 98
Modelled: 102
Confidence: 99.0%
Identity: 10%
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

Phyre2
4 |
| c6paxA_ |

### PDB 6pax chain A

Region: 2 - 103
Aligned: 100
Modelled: 102
Confidence: 99.0%
Identity: 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

Phyre2
5 |
| c1hlvA_ |

### PDB 1hlv chain A

Region: 1 - 106
Aligned: 106
Modelled: 106
Confidence: 98.7%
Identity: 16%
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

Phyre2
6 |
| d1pdnc_ |

### PDB 1pdn chain C

Region: 6 - 101
Aligned: 95
Modelled: 96
Confidence: 98.7%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
7 |
| c2k27A_ |

### PDB 2k27 chain A

Region: 1 - 103
Aligned: 101
Modelled: 103
Confidence: 98.1%
Identity: 14%
PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain

Phyre2
8 |
| d6paxa1 |

### PDB 6pax chain A domain 1

Region: 6 - 50
Aligned: 44
Modelled: 45
Confidence: 97.9%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
9 |
| d1k78a1 |

### PDB 1k78 chain A domain 1

Region: 6 - 50
Aligned: 44
Modelled: 45
Confidence: 97.9%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
10 |
| c3hosA_ |

### PDB 3hos chain A

Region: 7 - 103
Aligned: 96
Modelled: 97
Confidence: 97.9%
Identity: 10%
PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg

Phyre2
11 |
| d1hlva1 |

### PDB 1hlv chain A domain 1

Region: 1 - 44
Aligned: 44
Modelled: 44
Confidence: 97.8%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Centromere-binding

Phyre2
12 |
| d1bw6a_ |

### PDB 1bw6 chain A

Region: 1 - 44
Aligned: 44
Modelled: 44
Confidence: 97.8%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Centromere-binding

Phyre2
13 |
| c2elhA_ |

### PDB 2elh chain A

Region: 1 - 44
Aligned: 43
Modelled: 44
Confidence: 97.7%
Identity: 14%
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

Phyre2
14 |
| d2coba1 |

### PDB 2cob chain A domain 1

Region: 4 - 44
Aligned: 41
Modelled: 41
Confidence: 97.4%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Psq domain

Phyre2
15 |
| c2gloA_ |

### PDB 2glo chain A

Region: 2 - 43
Aligned: 42
Modelled: 42
Confidence: 97.4%
Identity: 19%
PDB header:transcription/dna
Chain: A: PDB Molecule:brinker cg9653-pa;
PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer

Phyre2
16 |
| d1r8da_ |

### PDB 1r8d chain A

Region: 23 - 168
Aligned: 104
Modelled: 106
Confidence: 97.0%
Identity: 12%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2
17 |
| c2vz4A_ |

### PDB 2vz4 chain A

Region: 23 - 159
Aligned: 97
Modelled: 101
Confidence: 96.5%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional activator tipa;
PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna

Phyre2
18 |
| c3hefB_ |

### PDB 3hef chain B

Region: 61 - 107
Aligned: 46
Modelled: 47
Confidence: 96.4%
Identity: 20%
PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit

Phyre2
19 |
| d1q06a_ |

### PDB 1q06 chain A

Region: 23 - 166
Aligned: 109
Modelled: 109
Confidence: 96.3%
Identity: 11%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2
20 |
| c3hh0C_ |

### PDB 3hh0 chain C

Region: 22 - 173
Aligned: 113
Modelled: 116
Confidence: 96.1%
Identity: 7%
PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2jn6a1 |
|  | 99.5 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like
2 | c2rn7A_ |
|  | 99.4 | 24 | 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
3 | c1u78A_ |
|  | 99.0 | 10 | 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
4 | c6paxA_ |
|  | 99.0 | 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
5 | c1hlvA_ |
|  | 98.7 | 16 | 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
6 | d1pdnc_ |
|  | 98.7 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
7 | c2k27A_ |
|  | 98.1 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain
8 | d6paxa1 |
|  | 97.9 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
9 | d1k78a1 |
|  | 97.9 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
10 | c3hosA_ |
|  | 97.9 | 10 | PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
11 | d1hlva1 |
|  | 97.8 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
12 | d1bw6a_ |
|  | 97.8 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
13 | c2elhA_ |
|  | 97.7 | 14 | 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
14 | d2coba1 |
|  | 97.4 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain
15 | c2gloA_ |
|  | 97.4 | 19 | PDB header:transcription/dna Chain: A: PDB Molecule:brinker cg9653-pa; PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer
16 | d1r8da_ |
|  | 97.0 | 12 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
17 | c2vz4A_ |
|  | 96.5 | 16 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator tipa; PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna
18 | c3hefB_ |
|  | 96.4 | 20 | PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
19 | d1q06a_ |
|  | 96.3 | 11 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
20 | c3hh0C_ |
|  | 96.1 | 7 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
21 | c3oouA_ |
| not modelled | 96.1 | 8 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua
22 | c2k9sA_ |
| not modelled | 96.1 | 11 | PDB header:transcription Chain: A: PDB Molecule:arabinose operon regulatory protein; PDBTitle: solution structure of dna binding domain of e. coli arac
23 | c3gpvA_ |
| not modelled | 96.1 | 8 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
24 | c3oioA_ |
| not modelled | 96.0 | 15 | 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
25 | d1r8ea1 |
| not modelled | 95.9 | 10 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
26 | c3mklB_ |
| not modelled | 95.7 | 7 | PDB header:transcription regulator Chain: B: PDB Molecule:hth-type transcriptional regulator gadx; PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
27 | c3lsgD_ |
| not modelled | 95.4 | 7 | PDB header:transcription regulator Chain: D: PDB Molecule:two-component response regulator yesn; PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586
28 | c1iufA_ |
| not modelled | 95.4 | 16 | PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein
29 | c3gbgA_ |
| not modelled | 95.3 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395
30 | c3gp4B_ |
| not modelled | 95.3 | 15 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes
31 | c2zhhA_ |
| not modelled | 95.2 | 18 | PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr
32 | d2oa4a1 |
| not modelled | 95.1 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:SPO1678-like
33 | d1vz0a1 |
| not modelled | 94.7 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like
34 | c2jmlA_ |
| not modelled | 94.5 | 19 | PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor
35 | c2jrtA_ |
| not modelled | 94.3 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr solution structure of the protein coded by gene2 rhos4_12090 of rhodobacter sphaeroides. northeast3 structural genomics target rhr5
36 | d1jhfa1 |
| not modelled | 94.2 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain
37 | c2w48D_ |
| not modelled | 94.1 | 28 | PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
38 | c3mn2B_ |
| not modelled | 94.0 | 12 | 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
39 | d1r1ua_ |
| not modelled | 93.6 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
40 | d1fipa_ |
| not modelled | 93.5 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
41 | c1bl0A_ |
| not modelled | 93.2 | 14 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
42 | c3qaoA_ |
| not modelled | 93.1 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:merr-like transcriptional regulator; PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e
43 | d1ntca_ |
| not modelled | 92.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
44 | c2o8xA_ |
| not modelled | 92.4 | 20 | 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
45 | d1rp3a2 |
| not modelled | 92.4 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
46 | c2l0kA_ |
| not modelled | 92.0 | 21 | 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
47 | c3d6zA_ |
| not modelled | 92.0 | 16 | PDB header:transcription regulator/dna Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator; PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine
48 | c2r0qF_ |
| not modelled | 91.9 | 13 | PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
49 | c1d5yD_ |
| not modelled | 91.7 | 11 | PDB header:transcription/dna Chain: D: PDB Molecule:rob transcription factor; PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna
50 | c2cg4B_ |
| not modelled | 91.7 | 12 | PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc
51 | d1stza1 |
| not modelled | 91.6 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
52 | c3e7lD_ |
| not modelled | 91.4 | 16 | PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
53 | d1xsva_ |
| not modelled | 91.1 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
54 | d1umqa_ |
| not modelled | 91.1 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
55 | c1umqA_ |
| not modelled | 91.1 | 16 | PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
56 | d1or7a1 |
| not modelled | 90.8 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
57 | d1jhga_ |
| not modelled | 90.8 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
58 | d1trra_ |
| not modelled | 90.8 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
59 | c1r22B_ |
| not modelled | 90.7 | 10 | 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
60 | c3frwF_ |
| not modelled | 90.6 | 22 | PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
61 | c3hugA_ |
| not modelled | 90.5 | 15 | 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
62 | c2e7xA_ |
| not modelled | 90.2 | 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
63 | c3korD_ |
| not modelled | 90.0 | 18 | PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
64 | c1or7A_ |
| not modelled | 90.0 | 17 | 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
65 | c2gm4B_ |
| not modelled | 89.9 | 9 | PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
66 | d1etxa_ |
| not modelled | 89.8 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
67 | c3mzyA_ |
| not modelled | 89.7 | 14 | PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
68 | c3i4pA_ |
| not modelled | 89.4 | 21 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
69 | c2cfxD_ |
| not modelled | 89.4 | 14 | PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc
70 | c2oqgA_ |
| not modelled | 89.2 | 14 | PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
71 | c3op9A_ |
| not modelled | 89.0 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua
72 | d1r1ta_ |
| not modelled | 89.0 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
73 | c3jthA_ |
| not modelled | 88.9 | 11 | PDB header:transcription Chain: A: PDB Molecule:transcription activator hlyu; PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
74 | d1x57a1 |
| not modelled | 88.8 | 8 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like
75 | c2kpjA_ |
| not modelled | 88.7 | 18 | 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
76 | d2ezla_ |
| not modelled | 88.4 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain
77 | d1ulya_ |
| not modelled | 88.4 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Hypothetical protein PH1932
78 | d1s7oa_ |
| not modelled | 88.3 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
79 | c1i1gA_ |
| not modelled | 87.5 | 16 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
80 | c2p6tH_ |
| not modelled | 87.5 | 9 | 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
81 | c3pqkD_ |
| not modelled | 87.5 | 10 | PDB header:transcription Chain: D: PDB Molecule:biofilm growth-associated repressor; PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
82 | d1g2ha_ |
| not modelled | 87.5 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
83 | c3f6oB_ |
| not modelled | 87.3 | 9 | PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
84 | c1rp3G_ |
| not modelled | 87.0 | 11 | PDB header:transcription Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia); PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm
85 | d1ijwc_ |
| not modelled | 87.0 | 5 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain
86 | c2jscB_ |
| not modelled | 86.2 | 12 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
87 | d1y9qa1 |
| not modelled | 86.2 | 8 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain
88 | c3b7hA_ |
| not modelled | 85.9 | 15 | PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11
89 | d2b5aa1 |
| not modelled | 85.9 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
90 | c1rr7A_ |
| not modelled | 85.7 | 10 | PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu
91 | d1rr7a_ |
| not modelled | 85.7 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor
92 | d1hcra_ |
| not modelled | 85.6 | 5 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain
93 | c1vz0B_ |
| not modelled | 85.4 | 18 | PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus
94 | d2ao9a1 |
| not modelled | 85.2 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Nanomeric phage protein-like
95 | c3omtA_ |
| not modelled | 85.1 | 10 | 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.
96 | c3t76A_ |
| not modelled | 85.0 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii
97 | c3f6vA_ |
| not modelled | 84.9 | 10 | PDB header:transcription regulator Chain: A: PDB Molecule:possible transcriptional regulator, arsr family PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
98 | c2ia0A_ |
| not modelled | 84.9 | 7 | 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)
99 | d1biaa1 |
| not modelled | 84.9 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
100 | d1i1ga1 |
| not modelled | 84.7 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
101 | c2kkoB_ |
| not modelled | 84.6 | 10 | PDB header:dna binding protein Chain: B: PDB Molecule:possible transcriptional regulatory protein PDBTitle: solution nmr structure of the homodimeric winged helix-turn-2 helix dna-binding domain (fragment 1-100) mb0332 from3 mycobacterium bovis, a possible arsr-family transcriptional4 regulator. northeast structural genomics consortium target5 mbr242e.
102 | c3bs3A_ |
| not modelled | 84.4 | 14 | 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
103 | c2l4aA_ |
| not modelled | 83.9 | 24 | 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
104 | c3bd1B_ |
| not modelled | 83.9 | 16 | 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
105 | c3fmyA_ |
| not modelled | 83.7 | 20 | 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)
106 | c3cuoB_ |
| not modelled | 83.5 | 10 | 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
107 | d1utxa_ |
| not modelled | 83.2 | 13 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
108 | d1y7ya1 |
| not modelled | 83.1 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
109 | c2ewtA_ |
| not modelled | 83.1 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd
110 | d1sq8a_ |
| not modelled | 83.0 | 6 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
111 | c2dbbA_ |
| not modelled | 82.5 | 15 | PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061
112 | c2xcjB_ |
| not modelled | 82.4 | 16 | 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
113 | c2h09A_ |
| not modelled | 82.3 | 15 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator mntr; PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
114 | c3dnvB_ |
| not modelled | 82.2 | 5 | PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein
115 | c2fjrB_ |
| not modelled | 82.0 | 21 | PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186
116 | d1adra_ |
| not modelled | 82.0 | 3 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
117 | d2a6ca1 |
| not modelled | 81.7 | 14 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
118 | d1r69a_ |
| not modelled | 81.2 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
119 | d2ppxa1 |
| not modelled | 81.2 | 10 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
120 | c2ppxA_ |
| not modelled | 81.2 | 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

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