Phyre 2 Results for Q47718

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | Q47718
Date | Thu Jan 5 12:37:09 GMT 2012
Unique Job ID | 871c808457684bec

Summary |

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

Model (left) based on template c1c0mA_
Top template information
PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase
Confidence and coverage
Confidence: | 99.6% | Coverage: | 43%
86 residues ( 43% of your sequence) have been modelled with 99.6% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
172 residues ( 87%) 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 | P | F | Y | F | R | K | E | C | P | L | N | S | G | Y | L | R | K | N | R | P | E | K | P | D | G | R | R | A | V | L | R | S | Q | V | L | E | L | H | G | I | S | H | G | S | A | G | A | R | S | I | A | T | M | A | T | R | R | G | Y
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | M | G | R | W | L | A | G | R | L | M | K | E | L | G | L | V | S | C | Q | Q | P | T | H | R | Y | K | R | G | G | H | E | H | V | A | I | P | N | Y | L | E | R | Q | F | A | V | T | E | P | N | Q | V | W | C | G | D | V | T | Y | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  | ? |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | W | T | G | K | R | W | A | Y | L | A | V | V | L | D | L | F | A | R | K | P | V | G | W | A | M | S | F | S | P | D | S | R | L | T | M | K | A | L | E | M | A | W | E | T | R | G | K | P | V | G | V | M | F | Q | A | I | K | A | V | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | .
Sequence |  | I | R | A | G | S | S | G | S | Y | C | G | D | T | G | S | G | R | V
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 |
| c1c0mA_ |

### PDB 1c0m chain A

Region: 106 - 194
Aligned: 86
Modelled: 89
Confidence: 99.6%
Identity: 19%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2
2 |
| d1asua_ |

### PDB 1asu chain A

Region: 102 - 197
Aligned: 93
Modelled: 96
Confidence: 99.5%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
3 |
| d1cxqa_ |

### PDB 1cxq chain A

Region: 107 - 197
Aligned: 88
Modelled: 91
Confidence: 99.5%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
4 |
| d1c0ma2 |

### PDB 1c0m chain A domain 2

Region: 103 - 194
Aligned: 89
Modelled: 92
Confidence: 99.4%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
5 |
| d1bcoa2 |

### PDB 1bco chain A domain 2

Region: 108 - 194
Aligned: 87
Modelled: 87
Confidence: 99.3%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2
6 |
| d1exqa_ |

### PDB 1exq chain A

Region: 107 - 194
Aligned: 79
Modelled: 88
Confidence: 99.0%
Identity: 11%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
7 |
| c3nf9A_ |

### PDB 3nf9 chain A

Region: 109 - 198
Aligned: 82
Modelled: 90
Confidence: 99.0%
Identity: 11%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design

Phyre2
8 |
| d1c6va_ |

### PDB 1c6v chain A

Region: 107 - 197
Aligned: 83
Modelled: 91
Confidence: 99.0%
Identity: 10%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
9 |
| c1ex4A_ |

### PDB 1ex4 chain A

Region: 107 - 194
Aligned: 79
Modelled: 88
Confidence: 98.9%
Identity: 11%
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain

Phyre2
10 |
| c3f9kV_ |

### PDB 3f9k chain V

Region: 109 - 197
Aligned: 81
Modelled: 89
Confidence: 98.9%
Identity: 10%
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd

Phyre2
11 |
| c1k6yB_ |

### PDB 1k6y chain B

Region: 32 - 197
Aligned: 124
Modelled: 140
Confidence: 98.9%
Identity: 9%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2
12 |
| c3kksB_ |

### PDB 3kks chain B

Region: 111 - 194
Aligned: 76
Modelled: 84
Confidence: 98.7%
Identity: 11%
PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii

Phyre2
13 |
| c1bcoA_ |

### PDB 1bco chain A

Region: 125 - 195
Aligned: 71
Modelled: 71
Confidence: 98.7%
Identity: 14%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2
14 |
| c3hpgC_ |

### PDB 3hpg chain C

Region: 32 - 194
Aligned: 121
Modelled: 137
Confidence: 98.6%
Identity: 13%
PDB header:transferase
Chain: C: PDB Molecule:integrase;
PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces

Phyre2
15 |
| c3dlrA_ |

### PDB 3dlr chain A

Region: 107 - 194
Aligned: 84
Modelled: 88
Confidence: 98.5%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase

Phyre2
16 |
| d1hyva_ |

### PDB 1hyv chain A

Region: 109 - 189
Aligned: 72
Modelled: 81
Confidence: 98.5%
Identity: 10%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2
17 |
| c3l2tB_ |

### PDB 3l2t chain B

Region: 106 - 194
Aligned: 85
Modelled: 89
Confidence: 98.3%
Identity: 13%
PDB header:recombination/dna
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)

Phyre2
18 |
| c3hosA_ |

### PDB 3hos chain A

Region: 32 - 194
Aligned: 157
Modelled: 163
Confidence: 97.4%
Identity: 11%
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
19 |
| c3v4gA_ |

### PDB 3v4g chain A

Region: 27 - 166
Aligned: 132
Modelled: 140
Confidence: 95.4%
Identity: 14%
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

Phyre2
20 |
| c1u78A_ |

### PDB 1u78 chain A

Region: 7 - 75
Aligned: 64
Modelled: 69
Confidence: 94.6%
Identity: 11%
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
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 |
60 |
61 |
62 |
63 |
64 |
65 |
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 |
75 |
76 |
77 |
78 |
79 |
80 |
81 |
82 |
83 |
84 |
85 |
86 |
87 |
88 |
89 |
90 |
91 |
92 |
93 |
94 |
95 |
96 |
97 |
98 |
99 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1c0mA_ |
|  | 99.6 | 19 | PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase
2 | d1asua_ |
|  | 99.5 | 18 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
3 | d1cxqa_ |
|  | 99.5 | 18 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
4 | d1c0ma2 |
|  | 99.4 | 18 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
5 | d1bcoa2 |
|  | 99.3 | 16 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain
6 | d1exqa_ |
|  | 99.0 | 11 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
7 | c3nf9A_ |
|  | 99.0 | 11 | PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
8 | d1c6va_ |
|  | 99.0 | 10 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
9 | c1ex4A_ |
|  | 98.9 | 11 | PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
10 | c3f9kV_ |
|  | 98.9 | 10 | PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
11 | c1k6yB_ |
|  | 98.9 | 9 | PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
12 | c3kksB_ |
|  | 98.7 | 11 | PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii
13 | c1bcoA_ |
|  | 98.7 | 14 | PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain
14 | c3hpgC_ |
|  | 98.6 | 13 | PDB header:transferase Chain: C: PDB Molecule:integrase; PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces
15 | c3dlrA_ |
|  | 98.5 | 14 | PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
16 | d1hyva_ |
|  | 98.5 | 10 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain
17 | c3l2tB_ |
|  | 98.3 | 13 | PDB header:recombination/dna Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)
18 | c3hosA_ |
|  | 97.4 | 11 | 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
19 | c3v4gA_ |
|  | 95.4 | 14 | 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
20 | c1u78A_ |
|  | 94.6 | 11 | 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
21 | d1aoya_ |
| not modelled | 93.8 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
22 | c1b4aA_ |
| not modelled | 93.2 | 16 | PDB header:repressor Chain: A: PDB Molecule:arginine repressor; PDBTitle: structure of the arginine repressor from bacillus stearothermophilus
23 | c3ereD_ |
| not modelled | 92.1 | 17 | 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
24 | c6paxA_ |
| not modelled | 92.0 | 12 | 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
25 | d1pdnc_ |
| not modelled | 87.1 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
26 | d1b4aa1 |
| not modelled | 86.6 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
27 | d2p5ka1 |
| not modelled | 86.2 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
28 | d1f9na1 |
| not modelled | 85.6 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
29 | c3mwmA_ |
| not modelled | 84.3 | 19 | PDB header:transcription Chain: A: PDB Molecule:putative metal uptake regulation protein; PDBTitle: graded expression of zinc-responsive genes through two regulatory2 zinc-binding sites in zur
30 | c2o03A_ |
| not modelled | 83.4 | 17 | PDB header:gene regulation Chain: A: PDB Molecule:probable zinc uptake regulation protein furb; PDBTitle: crystal structure of furb from m. tuberculosis- a zinc uptake2 regulator
31 | c2o8kA_ |
| not modelled | 83.0 | 17 | PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element
32 | c2fe3B_ |
| not modelled | 80.8 | 16 | PDB header:dna binding protein Chain: B: PDB Molecule:peroxide operon regulator; PDBTitle: the crystal structure of bacillus subtilis perr-zn reveals a novel2 zn(cys)4 structural redox switch
33 | c2xigA_ |
| not modelled | 79.6 | 14 | PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites
34 | d1mzba_ |
| not modelled | 79.5 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FUR-like
35 | c2w57A_ |
| not modelled | 72.8 | 16 | PDB header:metal transport Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: crystal structure of the vibrio cholerae ferric uptake2 regulator (fur) reveals structural rearrangement of the3 dna-binding domains
36 | c2r0qF_ |
| not modelled | 72.8 | 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
37 | c3f2kB_ |
| not modelled | 68.3 | 11 | PDB header:transferase Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar; PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar
38 | c2fu4B_ |
| not modelled | 66.8 | 16 | PDB header:dna binding protein Chain: B: PDB Molecule:ferric uptake regulation protein; PDBTitle: crystal structure of the dna binding domain of e.coli fur (ferric2 uptake regulator)
39 | d1nkua_ |
| not modelled | 64.4 | 23 | Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag)
40 | d1stza1 |
| not modelled | 63.7 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
41 | c2jg6A_ |
| not modelled | 62.6 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of a 3-methyladenine dna glycosylase i2 from staphylococcus aureus
42 | c3eyyA_ |
| not modelled | 56.4 | 19 | PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition
43 | c2xzmO_ |
| not modelled | 55.3 | 13 | PDB header:ribosome Chain: O: PDB Molecule:rps13e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1
44 | c2f7tA_ |
| not modelled | 46.5 | 11 | PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase
45 | d1u17a1 |
| not modelled | 43.6 | 8 | Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like
46 | c1hlvA_ |
| not modelled | 42.4 | 20 | 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
47 | d1x8qa_ |
| not modelled | 39.6 | 6 | Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like
48 | d2fi9a1 |
| not modelled | 35.2 | 5 | Fold:MTH938-like Superfamily:MTH938-like Family:MTH938-like
49 | d2fvta1 |
| not modelled | 33.8 | 6 | Fold:MTH938-like Superfamily:MTH938-like Family:MTH938-like
50 | d1nhpa3 |
| not modelled | 22.6 | 16 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
51 | c2i8bB_ |
| not modelled | 22.3 | 12 | PDB header:viral protein Chain: B: PDB Molecule:minor nucleoprotein vp30; PDBTitle: crystal structure of the c-terminal domain of ebola virus vp30
52 | c3r1fO_ |
| not modelled | 20.8 | 11 | PDB header:transcription Chain: O: PDB Molecule:esx-1 secretion-associated regulator espr; PDBTitle: crystal structure of a key regulator of virulence in mycobacterium2 tuberculosis
53 | d1dxla3 |
| not modelled | 20.0 | 10 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
54 | d1ebda3 |
| not modelled | 19.2 | 17 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
55 | c2rpiA_ |
| not modelled | 18.7 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease h; PDBTitle: the nmr structure of the submillisecond folding2 intermediate of the thermus thermophilus ribonuclease h
56 | d3grsa3 |
| not modelled | 18.2 | 16 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
57 | d1gesa3 |
| not modelled | 15.2 | 12 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
58 | d1ekja_ |
| not modelled | 15.0 | 16 | Fold:Resolvase-like Superfamily:beta-carbonic anhydrase, cab Family:beta-carbonic anhydrase, cab
59 | d1pm1x_ |
| not modelled | 14.4 | 9 | Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like
60 | d1lvla3 |
| not modelled | 13.3 | 14 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
61 | c3p9kD_ |
| not modelled | 12.5 | 8 | PDB header:transferase Chain: D: PDB Molecule:caffeic acid o-methyltransferase; PDBTitle: crystal structure of perennial ryegrass lpomt1 complexed with s-2 adenosyl-l-homocysteine and coniferaldehyde
62 | d1y1xa_ |
| not modelled | 12.4 | 9 | Fold:EF Hand-like Superfamily:EF-hand Family:Penta-EF-hand proteins
63 | c2jsoA_ |
| not modelled | 11.6 | 8 | PDB header:signaling protein Chain: A: PDB Molecule:polymyxin resistance protein pmrd; PDBTitle: antimicrobial resistance protein
64 | c3izbO_ |
| not modelled | 11.6 | 16 | PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein rps13 (s15p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
65 | d1lpfa3 |
| not modelled | 10.6 | 12 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
66 | d2i52a1 |
| not modelled | 10.4 | 10 | Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like
67 | c3lasA_ |
| not modelled | 10.2 | 11 | PDB header:lyase Chain: A: PDB Molecule:putative carbonic anhydrase; PDBTitle: crystal structure of carbonic anhydrase from streptococcus mutans to2 1.4 angstrom resolution
68 | d2coba1 |
| not modelled | 9.9 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain
69 | d1v59a3 |
| not modelled | 9.9 | 12 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
70 | d1ixsb1 |
| not modelled | 9.3 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain
71 | d1aoga3 |
| not modelled | 9.3 | 3 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
72 | d1u3em2 |
| not modelled | 8.9 | 11 | Fold:DNA-binding domain of intron-encoded endonucleases Superfamily:DNA-binding domain of intron-encoded endonucleases Family:DNA-binding domain of intron-encoded endonucleases
73 | c2qv5A_ |
| not modelled | 8.9 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu2773; PDBTitle: crystal structure of uncharacterized protein atu2773 from2 agrobacterium tumefaciens c58
74 | c1fpqA_ |
| not modelled | 8.3 | 5 | PDB header:transferase Chain: A: PDB Molecule:isoliquiritigenin 2'-o-methyltransferase; PDBTitle: crystal structure analysis of selenomethionine substituted chalcone o-2 methyltransferase
75 | d1onfa3 |
| not modelled | 8.3 | 14 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
76 | d1ojta3 |
| not modelled | 8.1 | 12 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
77 | c2a5vB_ |
| not modelled | 8.0 | 8 | PDB header:lyase Chain: B: PDB Molecule:carbonic anhydrase (carbonate dehydratase) (carbonic PDBTitle: crystal structure of m. tuberculosis beta carbonic anhydrase, rv3588c,2 tetrameric form
78 | c2j89A_ |
| not modelled | 8.0 | 7 | PDB header:oxidoreductase Chain: A: PDB Molecule:methionine sulfoxide reductase a; PDBTitle: functional and structural aspects of poplar cytosolic and2 plastidial type a methionine sulfoxide reductases
79 | d1ej5a_ |
| not modelled | 7.9 | 20 | Fold:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
80 | d1ixrc1 |
| not modelled | 7.8 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain
81 | d3lada3 |
| not modelled | 7.6 | 14 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
82 | d1ff3a_ |
| not modelled | 7.4 | 18 | Fold:Ferredoxin-like Superfamily:Peptide methionine sulfoxide reductase Family:Peptide methionine sulfoxide reductase
83 | d1feca3 |
| not modelled | 7.4 | 10 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
84 | d1gkab_ |
| not modelled | 7.3 | 16 | Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like
85 | d1in4a1 |
| not modelled | 7.2 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain
86 | c2k27A_ |
| not modelled | 7.2 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain
87 | c1ylkA_ |
| not modelled | 7.2 | 4 | PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein rv1284/mt1322; PDBTitle: crystal structure of rv1284 from mycobacterium tuberculosis in complex2 with thiocyanate
88 | c1fvaA_ |
| not modelled | 7.1 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:peptide methionine sulfoxide reductase; PDBTitle: crystal structure of bovine methionine sulfoxide reductase
89 | c2e4jA_ |
| not modelled | 7.0 | 10 | PDB header:isomerase Chain: A: PDB Molecule:prostaglandin-h2 d-isomerase; PDBTitle: solution structure of mouse lipocalin-type prostaglandin d2 synthase
90 | c1zgaA_ |
| not modelled | 6.9 | 9 | PDB header:plant protein, transferase Chain: A: PDB Molecule:isoflavanone 4'-o-methyltransferase'; PDBTitle: crystal structure of isoflavanone 4'-o-methyltransferase complexed2 with (+)-6a-hydroxymaackiain
91 | c3g43F_ |
| not modelled | 6.9 | 12 | PDB header:metal binding protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: crystal structure of the calmodulin-bound cav1.2 c-terminal2 regulatory domain dimer
92 | c3elkA_ |
| not modelled | 6.8 | 10 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcriptional regulator ta0346; PDBTitle: crystal structure of putative transcriptional regulator ta0346 from2 thermoplasma acidophilum
93 | c3klbA_ |
| not modelled | 6.8 | 17 | PDB header:flavoprotein Chain: A: PDB Molecule:putative flavoprotein; PDBTitle: crystal structure of putative flavoprotein in complex with fmn2 (yp_213683.1) from bacteroides fragilis nctc 9343 at 1.75 a3 resolution
94 | d1fp2a2 |
| not modelled | 6.6 | 5 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Plant O-methyltransferase, C-terminal domain
95 | c3icrA_ |
| not modelled | 6.4 | 6 | PDB header:oxidoreductase Chain: A: PDB Molecule:coenzyme a-disulfide reductase; PDBTitle: crystal structure of oxidized bacillus anthracis coadr-rhd
96 | c3eyxB_ |
| not modelled | 6.3 | 14 | PDB header:lyase Chain: B: PDB Molecule:carbonic anhydrase; PDBTitle: crystal structure of carbonic anhydrase nce103 from2 saccharomyces cerevisiae
97 | c2a8cE_ |
| not modelled | 6.2 | 5 | PDB header:lyase Chain: E: PDB Molecule:carbonic anhydrase 2; PDBTitle: haemophilus influenzae beta-carbonic anhydrase
98 | c3ucoB_ |
| not modelled | 6.1 | 13 | PDB header:lyase/lyase inhibitor Chain: B: PDB Molecule:carbonic anhydrase; PDBTitle: coccomyxa beta-carbonic anhydrase in complex with iodide
99 | c3hhhA_ |
| not modelled | 5.9 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, padr family; PDBTitle: crystal structure of transcriptional regulator, a member of padr2 family, from enterococcus faecalis v583

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
Disclaimer
Terms and Conditions
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