Phyre 2 Results for P0AFU8

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Email | l.a.kelley@imperial.ac.uk
Description | P0AFU8
Date | Thu Jan 5 11:27:19 GMT 2012
Unique Job ID | 2d5ea66f0091f510

Summary |

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

Model (left) based on template c1i8dB_
Top template information
PDB header:transferase Chain: B: PDB Molecule:riboflavin synthase; PDBTitle: crystal structure of riboflavin synthase
Confidence and coverage
Confidence: | 100.0% | Coverage: | 94%
201 residues ( 94% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | F | T | G | I | V | Q | G | T | A | K | L | V | S | I | D | E | K | P | N | F | R | T | H | V | V | E | L | P | D | H | M | L | D | G | L | E | T | G | A | S | V | A | H | N | G | C | C | L | T | V | T | E | I | N | G | N | H | V | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | F | D | L | M | K | E | T | L | R | I | T | N | L | G | D | L | K | V | G | D | W | V | N | V | E | R | A | A | K | F | S | D | E | I | G | G | H | L | M | S | G | H | I | M | T | T | A | E | V | A | K | I | L | T | S | E | N | N | R | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | I | W | F | K | V | Q | D | S | Q | L | M | K | Y | I | L | Y | K | G | F | I | G | I | D | G | I | S | L | T | V | G | E | V | T | P | T | R | F | C | V | H | L | I | P | E | T | L | E | R | T | T | L | G | K | K | K | L | G | A | R | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | .
Sequence |  | N | I | E | I | D | P | Q | T | Q | A | V | V | D | T | V | E | R | V | L | A | A | R | E | N | A | M | N | Q | P | G | T | E | A
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 |
| c1i8dB_ |

### PDB 1i8d chain B

Region: 1 - 206
Aligned: 201
Modelled: 201
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: B: PDB Molecule:riboflavin synthase;
PDBTitle: crystal structure of riboflavin synthase

Phyre2
2 |
| c1kzlA_ |

### PDB 1kzl chain A

Region: 1 - 202
Aligned: 202
Modelled: 202
Confidence: 100.0%
Identity: 35%
PDB header:transferase
Chain: A: PDB Molecule:riboflavin synthase;
PDBTitle: riboflavin synthase from s.pombe bound to2 carboxyethyllumazine

Phyre2
3 |
| c3a35B_ |

### PDB 3a35 chain B

Region: 1 - 184
Aligned: 182
Modelled: 184
Confidence: 100.0%
Identity: 31%
PDB header:luminescent protein
Chain: B: PDB Molecule:lumazine protein;
PDBTitle: crystal structure of lump complexed with riboflavin

Phyre2
4 |
| c3ddyA_ |

### PDB 3ddy chain A

Region: 1 - 184
Aligned: 173
Modelled: 184
Confidence: 100.0%
Identity: 32%
PDB header:luminescent protein
Chain: A: PDB Molecule:lumazine protein;
PDBTitle: structure of lumazine protein, an optical transponder of luminescent2 bacteria

Phyre2
5 |
| d1i8da2 |

### PDB 1i8d chain A domain 2

Region: 94 - 206
Aligned: 113
Modelled: 113
Confidence: 100.0%
Identity: 100%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Riboflavin synthase domain-like
Family: Riboflavin synthase

Phyre2
6 |
| d1kzla2 |

### PDB 1kzl chain A domain 2

Region: 93 - 202
Aligned: 110
Modelled: 110
Confidence: 100.0%
Identity: 33%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Riboflavin synthase domain-like
Family: Riboflavin synthase

Phyre2
7 |
| c1hzeB_ |

### PDB 1hze chain B

Region: 1 - 97
Aligned: 97
Modelled: 97
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: B: PDB Molecule:riboflavin synthase alpha chain;
PDBTitle: solution structure of the n-terminal domain of riboflavin synthase2 from e. coli

Phyre2
8 |
| c1i18B_ |

### PDB 1i18 chain B

Region: 1 - 97
Aligned: 97
Modelled: 97
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: B: PDB Molecule:riboflavin synthase alpha chain;
PDBTitle: solution structure of the n-terminal domain of riboflavin synthase2 from e. coli

Phyre2
9 |
| d1i8da1 |

### PDB 1i8d chain A domain 1

Region: 1 - 93
Aligned: 93
Modelled: 93
Confidence: 100.0%
Identity: 100%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Riboflavin synthase domain-like
Family: Riboflavin synthase

Phyre2
10 |
| c1pkvA_ |

### PDB 1pkv chain A

Region: 1 - 87
Aligned: 87
Modelled: 87
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: A: PDB Molecule:riboflavin synthase alpha chain;
PDBTitle: the n-terminal domain of riboflavin synthase in complex with2 riboflavin

Phyre2
11 |
| c1pkvB_ |

### PDB 1pkv chain B

Region: 1 - 87
Aligned: 87
Modelled: 87
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: B: PDB Molecule:riboflavin synthase alpha chain;
PDBTitle: the n-terminal domain of riboflavin synthase in complex with2 riboflavin

Phyre2
12 |
| d1kzla1 |

### PDB 1kzl chain A domain 1

Region: 1 - 92
Aligned: 92
Modelled: 92
Confidence: 100.0%
Identity: 38%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Riboflavin synthase domain-like
Family: Riboflavin synthase

Phyre2
13 |
| d2g50a1 |

### PDB 2g50 chain A domain 1

Region: 19 - 84
Aligned: 58
Modelled: 66
Confidence: 68.8%
Identity: 16%
Fold: PK beta-barrel domain-like
Superfamily: PK beta-barrel domain-like
Family: Pyruvate kinase beta-barrel domain

Phyre2
14 |
| c3nrfA_ |

### PDB 3nrf chain A

Region: 42 - 83
Aligned: 39
Modelled: 42
Confidence: 64.0%
Identity: 26%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:apag protein;
PDBTitle: crystal structure of an apag protein (pa1934) from pseudomonas2 aeruginosa pao1 at 1.50 a resolution

Phyre2
15 |
| d1pkla1 |

### PDB 1pkl chain A domain 1

Region: 17 - 84
Aligned: 61
Modelled: 68
Confidence: 48.6%
Identity: 11%
Fold: PK beta-barrel domain-like
Superfamily: PK beta-barrel domain-like
Family: Pyruvate kinase beta-barrel domain

Phyre2
16 |
| d1e0ta1 |

### PDB 1e0t chain A domain 1

Region: 19 - 84
Aligned: 58
Modelled: 66
Confidence: 46.2%
Identity: 31%
Fold: PK beta-barrel domain-like
Superfamily: PK beta-barrel domain-like
Family: Pyruvate kinase beta-barrel domain

Phyre2
17 |
| d1liua1 |

### PDB 1liu chain A domain 1

Region: 19 - 84
Aligned: 58
Modelled: 66
Confidence: 43.7%
Identity: 22%
Fold: PK beta-barrel domain-like
Superfamily: PK beta-barrel domain-like
Family: Pyruvate kinase beta-barrel domain

Phyre2
18 |
| d1a3xa1 |

### PDB 1a3x chain A domain 1

Region: 30 - 84
Aligned: 48
Modelled: 55
Confidence: 34.7%
Identity: 15%
Fold: PK beta-barrel domain-like
Superfamily: PK beta-barrel domain-like
Family: Pyruvate kinase beta-barrel domain

Phyre2
19 |
| c3o44G_ |

### PDB 3o44 chain G

Region: 81 - 91
Aligned: 11
Modelled: 11
Confidence: 33.8%
Identity: 36%
PDB header:toxin
Chain: G: PDB Molecule:hemolysin;
PDBTitle: crystal structure of the vibrio cholerae cytolysin (hlya) heptameric2 pore

Phyre2
20 |
| d2hx0a1 |

### PDB 2hx0 chain A domain 1

Region: 34 - 120
Aligned: 86
Modelled: 87
Confidence: 30.6%
Identity: 17%
Fold: AF0104/ALDC/Ptd012-like
Superfamily: AF0104/ALDC/Ptd012-like
Family: AF0104-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1i8dB_ |
|  | 100.0 | 100 | PDB header:transferase Chain: B: PDB Molecule:riboflavin synthase; PDBTitle: crystal structure of riboflavin synthase
2 | c1kzlA_ |
|  | 100.0 | 35 | PDB header:transferase Chain: A: PDB Molecule:riboflavin synthase; PDBTitle: riboflavin synthase from s.pombe bound to2 carboxyethyllumazine
3 | c3a35B_ |
|  | 100.0 | 31 | PDB header:luminescent protein Chain: B: PDB Molecule:lumazine protein; PDBTitle: crystal structure of lump complexed with riboflavin
4 | c3ddyA_ |
|  | 100.0 | 32 | PDB header:luminescent protein Chain: A: PDB Molecule:lumazine protein; PDBTitle: structure of lumazine protein, an optical transponder of luminescent2 bacteria
5 | d1i8da2 |
|  | 100.0 | 100 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Riboflavin synthase
6 | d1kzla2 |
|  | 100.0 | 33 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Riboflavin synthase
7 | c1hzeB_ |
|  | 100.0 | 100 | PDB header:transferase Chain: B: PDB Molecule:riboflavin synthase alpha chain; PDBTitle: solution structure of the n-terminal domain of riboflavin synthase2 from e. coli
8 | c1i18B_ |
|  | 100.0 | 100 | PDB header:transferase Chain: B: PDB Molecule:riboflavin synthase alpha chain; PDBTitle: solution structure of the n-terminal domain of riboflavin synthase2 from e. coli
9 | d1i8da1 |
|  | 100.0 | 100 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Riboflavin synthase
10 | c1pkvA_ |
|  | 100.0 | 100 | PDB header:transferase Chain: A: PDB Molecule:riboflavin synthase alpha chain; PDBTitle: the n-terminal domain of riboflavin synthase in complex with2 riboflavin
11 | c1pkvB_ |
|  | 100.0 | 100 | PDB header:transferase Chain: B: PDB Molecule:riboflavin synthase alpha chain; PDBTitle: the n-terminal domain of riboflavin synthase in complex with2 riboflavin
12 | d1kzla1 |
|  | 100.0 | 38 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Riboflavin synthase
13 | d2g50a1 |
|  | 68.8 | 16 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
14 | c3nrfA_ |
|  | 64.0 | 26 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:apag protein; PDBTitle: crystal structure of an apag protein (pa1934) from pseudomonas2 aeruginosa pao1 at 1.50 a resolution
15 | d1pkla1 |
|  | 48.6 | 11 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
16 | d1e0ta1 |
|  | 46.2 | 31 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
17 | d1liua1 |
|  | 43.7 | 22 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
18 | d1a3xa1 |
|  | 34.7 | 15 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
19 | c3o44G_ |
|  | 33.8 | 36 | PDB header:toxin Chain: G: PDB Molecule:hemolysin; PDBTitle: crystal structure of the vibrio cholerae cytolysin (hlya) heptameric2 pore
20 | d2hx0a1 |
|  | 30.6 | 17 | Fold:AF0104/ALDC/Ptd012-like Superfamily:AF0104/ALDC/Ptd012-like Family:AF0104-like
21 | d1pkma1 |
| not modelled | 29.2 | 20 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain
22 | c1xezA_ |
| not modelled | 28.2 | 36 | PDB header:toxin Chain: A: PDB Molecule:hemolysin; PDBTitle: crystal structure of the vibrio cholerae cytolysin (hlya)2 pro-toxin with octylglucoside bound
23 | c1hn0A_ |
| not modelled | 27.4 | 14 | PDB header:lyase Chain: A: PDB Molecule:chondroitin abc lyase i; PDBTitle: crystal structure of chondroitin abc lyase i from proteus2 vulgaris at 1.9 angstroms resolution
24 | d1zbfa1 |
| not modelled | 26.8 | 10 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H
25 | d3bzka4 |
| not modelled | 25.2 | 16 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
26 | d1hn0a3 |
| not modelled | 23.5 | 11 | Fold:Hyaluronate lyase-like, C-terminal domain Superfamily:Hyaluronate lyase-like, C-terminal domain Family:Hyaluronate lyase-like, C-terminal domain
27 | c1v0eB_ |
| not modelled | 20.2 | 26 | PDB header:hydrolase Chain: B: PDB Molecule:endo-alpha-sialidase; PDBTitle: endosialidase of bacteriophage k1f
28 | d1zrua1 |
| not modelled | 17.9 | 24 | Fold:Virus attachment protein globular domain Superfamily:Virus attachment protein globular domain Family:Lactophage receptor-binding protein head domain
29 | c2izpB_ |
| not modelled | 16.9 | 25 | PDB header:toxin Chain: B: PDB Molecule:putative membrane antigen; PDBTitle: bipd - an invasion prtein associated with the type-iii2 secretion system of burkholderia pseudomallei.
30 | d2izpa1 |
| not modelled | 15.4 | 25 | Fold:IpaD-like Superfamily:IpaD-like Family:IpaD-like
31 | d1vqoq1 |
| not modelled | 15.2 | 24 | Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:Ribosomal proteins L24p and L21e
32 | c3da0C_ |
| not modelled | 13.8 | 24 | PDB header:viral protein Chain: C: PDB Molecule:cleaved chimeric receptor binding protein from PDBTitle: crystal structure of a cleaved form of a chimeric receptor binding2 protein from lactococcal phages subspecies tp901-1 and p2
33 | c2khiA_ |
| not modelled | 13.7 | 10 | PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1
34 | c3h43F_ |
| not modelled | 13.2 | 20 | PDB header:hydrolase Chain: F: PDB Molecule:proteasome-activating nucleotidase; PDBTitle: n-terminal domain of the proteasome-activating nucleotidase2 of methanocaldococcus jannaschii
35 | c2zkrq_ |
| not modelled | 12.8 | 29 | PDB header:ribosomal protein/rna Chain: Q: PDB Molecule:rna expansion segment es31 part ii; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
36 | d1qfja1 |
| not modelled | 12.8 | 7 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like
37 | d1xpna_ |
| not modelled | 12.7 | 25 | Fold:Prealbumin-like Superfamily:Hypothetical protein PA1324 Family:Hypothetical protein PA1324
38 | c2jz2A_ |
| not modelled | 12.4 | 44 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ssl0352 protein; PDBTitle: solution nmr structure of ssl0352 protein from synechocystis sp. pcc2 6803. northeast structural genomics consortium target sgr42
39 | d1xsza2 |
| not modelled | 11.9 | 25 | Fold:TBP-like Superfamily:RalF, C-terminal domain Family:RalF, C-terminal domain
40 | d1yq2a3 |
| not modelled | 11.6 | 21 | Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:beta-Galactosidase/glucuronidase, N-terminal domain
41 | c3kf8D_ |
| not modelled | 11.4 | 27 | PDB header:structural protein Chain: D: PDB Molecule:protein ten1; PDBTitle: crystal structure of c. tropicalis stn1-ten1 complex
42 | c1s1iQ_ |
| not modelled | 11.2 | 35 | PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein l21-a; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.
43 | c2dycA_ |
| not modelled | 11.1 | 20 | PDB header:sugar binding protein Chain: A: PDB Molecule:galectin-4; PDBTitle: crystal structure of the n-terminal domain of mouse galectin-4
44 | d1ulea_ |
| not modelled | 10.9 | 12 | Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Galectin (animal S-lectin)
45 | d2f0ca1 |
| not modelled | 10.6 | 20 | Fold:Virus attachment protein globular domain Superfamily:Virus attachment protein globular domain Family:Lactophage receptor-binding protein head domain
46 | c3d8mA_ |
| not modelled | 10.4 | 24 | PDB header:virus/viral protein Chain: A: PDB Molecule:baseplate protein, receptor binding protein; PDBTitle: crystal structure of a chimeric receptor binding protein from2 lactococcal phages subspecies tp901-1 and p2
47 | d1s04a_ |
| not modelled | 10.2 | 22 | Fold:PUA domain-like Superfamily:PUA domain-like Family:ProFAR isomerase associated domain
48 | c3iz5U_ |
| not modelled | 9.4 | 29 | PDB header:ribosome Chain: U: PDB Molecule:60s ribosomal protein l21 (l21e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
49 | d1r9fa_ |
| not modelled | 9.4 | 36 | Fold:Tombusvirus P19 core protein, VP19 Superfamily:Tombusvirus P19 core protein, VP19 Family:Tombusvirus P19 core protein, VP19
50 | c2p6yA_ |
| not modelled | 9.3 | 22 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein vca0587; PDBTitle: x-ray structure of the protein q9km02_vibch from vibrio cholerae at2 the resolution 1.63 a. northeast structural genomics consortium3 target vcr80.
51 | c2r7fA_ |
| not modelled | 9.3 | 5 | PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease ii family protein; PDBTitle: crystal structure of ribonuclease ii family protein from deinococcus2 radiodurans, hexagonal crystal form. northeast structural genomics3 target drr63
52 | c3izcU_ |
| not modelled | 9.2 | 35 | PDB header:ribosome Chain: U: PDB Molecule:60s ribosomal protein rpl21 (l21e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
53 | c4a1aP_ |
| not modelled | 9.0 | 35 | PDB header:ribosome Chain: P: PDB Molecule:60s ribosomal protein l21; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3.
54 | d1cb8a2 |
| not modelled | 8.8 | 13 | Fold:Hyaluronate lyase-like, C-terminal domain Superfamily:Hyaluronate lyase-like, C-terminal domain Family:Hyaluronate lyase-like, C-terminal domain
55 | d1fnda1 |
| not modelled | 8.7 | 17 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like
56 | c2wg6L_ |
| not modelled | 8.1 | 22 | PDB header:transcription,hydrolase Chain: L: PDB Molecule:general control protein gcn4, PDBTitle: proteasome-activating nucleotidase (pan) n-domain (57-134)2 from archaeoglobus fulgidus fused to gcn4, p61a mutant
57 | c3htnA_ |
| not modelled | 7.9 | 17 | PDB header:metal binding protein Chain: A: PDB Molecule:putative dna binding protein; PDBTitle: crystal structure of a putative dna binding protein (bt_1116) from2 bacteroides thetaiotaomicron vpi-5482 at 1.50 a resolution
58 | d1krha1 |
| not modelled | 7.8 | 16 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like
59 | c2z14A_ |
| not modelled | 7.7 | 13 | PDB header:signaling protein Chain: A: PDB Molecule:ef-hand domain-containing family member c2; PDBTitle: crystal structure of the n-terminal duf1126 in human ef-2 hand domain containing 2 protein
60 | d1gawa1 |
| not modelled | 7.6 | 17 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like
61 | c3ca9A_ |
| not modelled | 7.5 | 21 | PDB header:hydrolase Chain: A: PDB Molecule:deoxyuridine triphosphatase; PDBTitle: evolution of chlorella virus dutpase
62 | d2plia1 |
| not modelled | 7.5 | 21 | Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like
63 | d2c9aa2 |
| not modelled | 7.4 | 23 | Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:MAM domain
64 | d2oaia1 |
| not modelled | 7.0 | 13 | Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like
65 | d1pk6a_ |
| not modelled | 6.9 | 17 | Fold:TNF-like Superfamily:TNF-like Family:TNF-like
66 | c1aqfB_ |
| not modelled | 6.9 | 17 | PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase; PDBTitle: pyruvate kinase from rabbit muscle with mg, k, and l-2 phospholactate
67 | d2p13a1 |
| not modelled | 6.7 | 14 | Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like
68 | c3ftjA_ |
| not modelled | 6.7 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:macrolide export atp-binding/permease protein PDBTitle: crystal structure of the periplasmic region of macb from2 actinobacillus actinomycetemcomitans
69 | c3m9bK_ |
| not modelled | 6.7 | 25 | PDB header:chaperone Chain: K: PDB Molecule:proteasome-associated atpase; PDBTitle: crystal structure of the amino terminal coiled coil domain and the2 inter domain of the mycobacterium tuberculosis proteasomal atpase mpa
70 | d1k8kg_ |
| not modelled | 6.5 | 14 | Fold:alpha-alpha superhelix Superfamily:Arp2/3 complex 16 kDa subunit ARPC5 Family:Arp2/3 complex 16 kDa subunit ARPC5
71 | d1fdra1 |
| not modelled | 6.4 | 16 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like
72 | c1t5aB_ |
| not modelled | 6.3 | 17 | PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase, m2 isozyme; PDBTitle: human pyruvate kinase m2
73 | c2khjA_ |
| not modelled | 6.3 | 13 | PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1
74 | d1j8hd1 |
| not modelled | 6.0 | 27 | Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like)
75 | d2plsa1 |
| not modelled | 6.0 | 17 | Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like
76 | c2k4vA_ |
| not modelled | 5.9 | 27 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein pa1076; PDBTitle: solution structure of uncharacterized protein pa1076 from2 pseudomonas aeruginosa. northeast structural genomics3 consortium (nesg) target pat3, ontario center for4 structural proteomics target pa1076 .
77 | d1duna_ |
| not modelled | 5.8 | 13 | Fold:beta-clip Superfamily:dUTPase-like Family:dUTPase-like
78 | c2l0dA_ |
| not modelled | 5.8 | 12 | PDB header:cell adhesion Chain: A: PDB Molecule:cell surface protein; PDBTitle: solution nmr structure of putative cell surface protein ma_4588 (272-2 376 domain) from methanosarcina acetivorans, northeast structural3 genomics consortium target mvr254a
79 | d1qfza1 |
| not modelled | 5.6 | 17 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like
80 | c3lgjA_ |
| not modelled | 5.4 | 20 | PDB header:dna binding protein Chain: A: PDB Molecule:single-stranded dna-binding protein; PDBTitle: crystal structure of single-stranded binding protein (ssb) from2 bartonella henselae
81 | c2zzfA_ |
| not modelled | 5.3 | 18 | PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of alanyl-trna synthetase without2 oligomerization domain
82 | c2aklA_ |
| not modelled | 5.3 | 30 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phna-like protein pa0128; PDBTitle: solution structure for phn-a like protein pa0128 from2 pseudomonas aeruginosa
83 | d3deda1 |
| not modelled | 5.1 | 17 | Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like
84 | d1am2a_ |
| not modelled | 5.0 | 19 | Fold:Hedgehog/intein (Hint) domain Superfamily:Hedgehog/intein (Hint) domain Family:Intein (protein splicing domain)
85 | c2vl6C_ |
| not modelled | 5.0 | 27 | PDB header:dna binding protein Chain: C: PDB Molecule:minichromosome maintenance protein mcm; PDBTitle: structural analysis of the sulfolobus solfataricus mcm2 protein n-terminal domain

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