Phyre 2 Results for P18472

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Email | l.a.kelley@imperial.ac.uk
Description | P18472
Date | Thu Jan 5 11:37:00 GMT 2012
Unique Job ID | 5279f5cb5050d57d

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2fu3A_
Top template information
PDB header:biosynthetic protein/structural protein Chain: A: PDB Molecule:gephyrin; PDBTitle: crystal structure of gephyrin e-domain
Confidence and coverage
Confidence: | 72.2% | Coverage: | 34%
71 residues ( 34% of your sequence) have been modelled with 72.2% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | R | C | R | G | L | I | A | L | L | I | W | G | Q | S | V | A | A | A | D | L | G | T | W | G | D | L | W | P | V | K | E | P | D | M | L | T | V | I | M | Q | R | L | T | A | L | E | Q | S | G | E | M | G | R | K | M | D | A | F | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | R | V | I | R | N | S | L | R | P | P | A | V | P | G | I | G | R | T | E | K | Y | G | S | R | L | F | D | P | S | V | R | L | A | A | D | I | R | D | N | E | G | R | V | F | A | R | Q | G | E | V | M | N | P | L | Q | Y | V | P | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | N | Q | T | L | Y | F | I | N | G | D | D | P | A | Q | V | A | W | M | K | R | Q | T | P | P | T | L | E | S | K | I | I | L | V | Q | G | S | I | P | E | M | Q | K | S | L | D | S | R | V | Y | F | D | Q | N | G | V | L | C | Q | R | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210
Sequence |  | G | I | D | Q | V | P | A | R | V | S | A | V | P | G | D | R | F | L | K | V | E | F | I | P | A | E | E | G | R | 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 |
| c2fu3A_ |

### PDB 2fu3 chain A

Region: 100 - 171
Aligned: 71
Modelled: 72
Confidence: 72.2%
Identity: 20%
PDB header:biosynthetic protein/structural protein
Chain: A: PDB Molecule:gephyrin;
PDBTitle: crystal structure of gephyrin e-domain

Phyre2
2 |
| c2bhvC_ |

### PDB 2bhv chain C

Region: 89 - 112
Aligned: 24
Modelled: 24
Confidence: 60.3%
Identity: 21%
PDB header:bacterial protein
Chain: C: PDB Molecule:comb10;
PDBTitle: structure of comb10 of the com type iv secretion system of2 helicobacter pylori

Phyre2
3 |
| c3jqoV_ |

### PDB 3jqo chain V

Region: 90 - 112
Aligned: 23
Modelled: 23
Confidence: 57.7%
Identity: 22%
PDB header:transport protein
Chain: V: PDB Molecule:traf protein;
PDBTitle: crystal structure of the outer membrane complex of a type iv2 secretion system

Phyre2
4 |
| d2gtta1 |

### PDB 2gtt chain A domain 1

Region: 102 - 118
Aligned: 17
Modelled: 17
Confidence: 57.5%
Identity: 29%
Fold: Rhabdovirus nucleoprotein-like
Superfamily: Rhabdovirus nucleoprotein-like
Family: Rhabdovirus nucleocapsid protein

Phyre2
5 |
| d2gica1 |

### PDB 2gic chain A domain 1

Region: 102 - 120
Aligned: 19
Modelled: 19
Confidence: 55.1%
Identity: 16%
Fold: Rhabdovirus nucleoprotein-like
Superfamily: Rhabdovirus nucleoprotein-like
Family: Rhabdovirus nucleocapsid protein

Phyre2
6 |
| c3emxB_ |

### PDB 3emx chain B

Region: 157 - 197
Aligned: 41
Modelled: 41
Confidence: 52.0%
Identity: 17%
PDB header:oxidoreductase
Chain: B: PDB Molecule:thioredoxin;
PDBTitle: crystal structure of thioredoxin from aeropyrum pernix

Phyre2
7 |
| c2nqqA_ |

### PDB 2nqq chain A

Region: 100 - 171
Aligned: 70
Modelled: 72
Confidence: 51.9%
Identity: 19%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:molybdopterin biosynthesis protein moea;
PDBTitle: moea r137q

Phyre2
8 |
| c2qsiB_ |

### PDB 2qsi chain B

Region: 157 - 197
Aligned: 41
Modelled: 41
Confidence: 50.2%
Identity: 20%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative hydrogenase expression/formation protein hupg;
PDBTitle: crystal structure of putative hydrogenase expression/formation protein2 hupg from rhodopseudomonas palustris cga009

Phyre2
9 |
| c3e7hA_ |

### PDB 3e7h chain A

Region: 92 - 114
Aligned: 23
Modelled: 23
Confidence: 47.7%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: the crystal structure of the beta subunit of the dna-2 directed rna polymerase from vibrio cholerae o1 biovar3 eltor

Phyre2
10 |
| d1j08a2 |

### PDB 1j08 chain A domain 2

Region: 171 - 207
Aligned: 37
Modelled: 37
Confidence: 47.2%
Identity: 19%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: PDI-like

Phyre2
11 |
| d2hfda1 |

### PDB 2hfd chain A domain 1

Region: 171 - 201
Aligned: 31
Modelled: 31
Confidence: 43.9%
Identity: 19%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: HyaE-like

Phyre2
12 |
| c2yjpB_ |

### PDB 2yjp chain B

Region: 24 - 73
Aligned: 50
Modelled: 50
Confidence: 41.7%
Identity: 14%
PDB header:transport protein
Chain: B: PDB Molecule:putative abc transporter, periplasmic binding protein,
PDBTitle: crystal structure of the solute receptors for l-cysteine of2 neisseria gonorrhoeae

Phyre2
13 |
| d1v58a1 |

### PDB 1v58 chain A domain 1

Region: 175 - 208
Aligned: 34
Modelled: 34
Confidence: 40.8%
Identity: 18%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: DsbC/DsbG C-terminal domain-like

Phyre2
14 |
| d1woua_ |

### PDB 1wou chain A

Region: 171 - 197
Aligned: 27
Modelled: 27
Confidence: 36.7%
Identity: 19%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Txnl5-like

Phyre2
15 |
| d1v9wa_ |

### PDB 1v9w chain A

Region: 157 - 197
Aligned: 41
Modelled: 41
Confidence: 36.3%
Identity: 27%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Txnl5-like

Phyre2
16 |
| d1hyua4 |

### PDB 1hyu chain A domain 4

Region: 171 - 189
Aligned: 19
Modelled: 19
Confidence: 36.0%
Identity: 16%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: PDI-like

Phyre2
17 |
| d1nhoa_ |

### PDB 1nho chain A

Region: 171 - 189
Aligned: 19
Modelled: 19
Confidence: 35.6%
Identity: 21%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Thioltransferase

Phyre2
18 |
| d1syra_ |

### PDB 1syr chain A

Region: 171 - 210
Aligned: 40
Modelled: 40
Confidence: 35.3%
Identity: 10%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Thioltransferase

Phyre2
19 |
| d1zmaa1 |

### PDB 1zma chain A domain 1

Region: 157 - 200
Aligned: 43
Modelled: 44
Confidence: 34.1%
Identity: 19%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Thioltransferase

Phyre2
20 |
| c2fgxA_ |

### PDB 2fgx chain A

Region: 171 - 197
Aligned: 26
Modelled: 27
Confidence: 33.7%
Identity: 19%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative thioredoxin;
PDBTitle: solution nmr structure of protein ne2328 from nitrosomonas2 europaea. northeast structural genomics consortium target3 net3.

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2fu3A_ |
|  | 72.2 | 20 | PDB header:biosynthetic protein/structural protein Chain: A: PDB Molecule:gephyrin; PDBTitle: crystal structure of gephyrin e-domain
2 | c2bhvC_ |
|  | 60.3 | 21 | PDB header:bacterial protein Chain: C: PDB Molecule:comb10; PDBTitle: structure of comb10 of the com type iv secretion system of2 helicobacter pylori
3 | c3jqoV_ |
|  | 57.7 | 22 | PDB header:transport protein Chain: V: PDB Molecule:traf protein; PDBTitle: crystal structure of the outer membrane complex of a type iv2 secretion system
4 | d2gtta1 |
|  | 57.5 | 29 | Fold:Rhabdovirus nucleoprotein-like Superfamily:Rhabdovirus nucleoprotein-like Family:Rhabdovirus nucleocapsid protein
5 | d2gica1 |
|  | 55.1 | 16 | Fold:Rhabdovirus nucleoprotein-like Superfamily:Rhabdovirus nucleoprotein-like Family:Rhabdovirus nucleocapsid protein
6 | c3emxB_ |
|  | 52.0 | 17 | PDB header:oxidoreductase Chain: B: PDB Molecule:thioredoxin; PDBTitle: crystal structure of thioredoxin from aeropyrum pernix
7 | c2nqqA_ |
|  | 51.9 | 19 | PDB header:biosynthetic protein Chain: A: PDB Molecule:molybdopterin biosynthesis protein moea; PDBTitle: moea r137q
8 | c2qsiB_ |
|  | 50.2 | 20 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative hydrogenase expression/formation protein hupg; PDBTitle: crystal structure of putative hydrogenase expression/formation protein2 hupg from rhodopseudomonas palustris cga009
9 | c3e7hA_ |
|  | 47.7 | 13 | PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta; PDBTitle: the crystal structure of the beta subunit of the dna-2 directed rna polymerase from vibrio cholerae o1 biovar3 eltor
10 | d1j08a2 |
|  | 47.2 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like
11 | d2hfda1 |
|  | 43.9 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:HyaE-like
12 | c2yjpB_ |
|  | 41.7 | 14 | PDB header:transport protein Chain: B: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the solute receptors for l-cysteine of2 neisseria gonorrhoeae
13 | d1v58a1 |
|  | 40.8 | 18 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbC/DsbG C-terminal domain-like
14 | d1woua_ |
|  | 36.7 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Txnl5-like
15 | d1v9wa_ |
|  | 36.3 | 27 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Txnl5-like
16 | d1hyua4 |
|  | 36.0 | 16 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like
17 | d1nhoa_ |
|  | 35.6 | 21 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
18 | d1syra_ |
|  | 35.3 | 10 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
19 | d1zmaa1 |
|  | 34.1 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
20 | c2fgxA_ |
|  | 33.7 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative thioredoxin; PDBTitle: solution nmr structure of protein ne2328 from nitrosomonas2 europaea. northeast structural genomics consortium target3 net3.
21 | c2vm2C_ |
| not modelled | 33.2 | 11 | PDB header:oxidoreductase Chain: C: PDB Molecule:thioredoxin h isoform 1.; PDBTitle: crystal structure of barley thioredoxin h isoform 12 crystallized using peg as precipitant
22 | d1j08a1 |
| not modelled | 31.6 | 23 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like
23 | d2nqra2 |
| not modelled | 31.4 | 18 | Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like
24 | c2l6dA_ |
| not modelled | 30.3 | 23 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: solution structure of desulfothioredoxin from desulfovibrio vulgaris2 hildenborough in its reduced form
25 | c2dizA_ |
| not modelled | 29.8 | 11 | PDB header:electron transport Chain: A: PDB Molecule:thioredoxin domain-containing protein 5; PDBTitle: the solution structure of the third thioredoxin domain of2 human thioredoxin domain-containing protein 5
26 | d1a8la1 |
| not modelled | 29.8 | 28 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like
27 | d1fo5a_ |
| not modelled | 29.8 | 32 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
28 | d1uz5a2 |
| not modelled | 29.4 | 29 | Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like
29 | c3nvbA_ |
| not modelled | 29.0 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of n-terminal part of the protein bf1531 from2 bacteroides fragilis containing phosphatase domain complexed with mg3 and tungstate
30 | d1h6ua1 |
| not modelled | 28.9 | 9 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Internalin Ig-like domain
31 | c3dmlA_ |
| not modelled | 28.4 | 16 | PDB header:oxidoreductase Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of the periplasmic thioredoxin soxs from2 paracoccus pantotrophus (reduced form)
32 | c2pptA_ |
| not modelled | 28.1 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin-2; PDBTitle: crystal structure of thioredoxin-2
33 | d1h6ta1 |
| not modelled | 28.0 | 5 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Internalin Ig-like domain
34 | c1v57A_ |
| not modelled | 27.6 | 18 | PDB header:isomerase Chain: A: PDB Molecule:thiol:disulfide interchange protein dsbg; PDBTitle: crystal structure of the disulfide bond isomerase dsbg
35 | c3gnjD_ |
| not modelled | 26.9 | 23 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:thioredoxin domain protein; PDBTitle: the crystal structure of a thioredoxin-related protein from2 desulfitobacterium hafniense dcb
36 | c3cxgA_ |
| not modelled | 26.6 | 20 | PDB header:oxidoreductase Chain: A: PDB Molecule:putative thioredoxin; PDBTitle: crystal structure of plasmodium falciparum thioredoxin, pfi0790w
37 | d1gh2a_ |
| not modelled | 26.2 | 13 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
38 | d1qgva_ |
| not modelled | 25.7 | 0 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:spliceosomal protein U5-15Kd
39 | d1spgb_ |
| not modelled | 25.5 | 8 | Fold:Globin-like Superfamily:Globin-like Family:Globins
40 | c2y7iB_ |
| not modelled | 25.3 | 19 | PDB header:arginine-binding protein Chain: B: PDB Molecule:stm4351; PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351.
41 | d1wu2a2 |
| not modelled | 25.2 | 33 | Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like
42 | c2l5lA_ |
| not modelled | 24.4 | 14 | PDB header:transport protein Chain: A: PDB Molecule:thioredoxin; PDBTitle: solution structure of thioredoxin from bacteroides vulgatus
43 | c2f51B_ |
| not modelled | 23.9 | 18 | PDB header:electron transport Chain: B: PDB Molecule:thioredoxin; PDBTitle: structure of trichomonas vaginalis thioredoxin
44 | c3d6iB_ |
| not modelled | 23.5 | 19 | PDB header:oxidoreductase Chain: B: PDB Molecule:monothiol glutaredoxin-3; PDBTitle: structure of the thioredoxin-like domain of yeast2 glutaredoxin 3
45 | d1a8la2 |
| not modelled | 23.5 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like
46 | c2dmlA_ |
| not modelled | 23.1 | 21 | PDB header:isomerase Chain: A: PDB Molecule:protein disulfide-isomerase a6; PDBTitle: the solution structure of the first thioredoxin domain of2 mouse protein disulfide-isomerase a6
47 | c3gv1A_ |
| not modelled | 22.3 | 21 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:disulfide interchange protein; PDBTitle: crystal structure of disulfide interchange protein from neisseria2 gonorrhoeae
48 | d1wdna_ |
| not modelled | 22.1 | 11 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
49 | d2omza1 |
| not modelled | 21.7 | 14 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Internalin Ig-like domain
50 | c1j08A_ |
| not modelled | 21.4 | 19 | PDB header:isomerase Chain: A: PDB Molecule:glutaredoxin-like protein; PDBTitle: crystal structure of glutaredoxin-like protein from2 pyrococcus horikoshii
51 | c2i9hA_ |
| not modelled | 20.7 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin i; PDBTitle: nmr solution structure of the reduced form of thioredoxin 12 from yeast (trx1)
52 | d2b5ea4 |
| not modelled | 20.7 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like
53 | c3kzqE_ |
| not modelled | 20.5 | 21 | PDB header:structural genomics, unknown function Chain: E: PDB Molecule:putative uncharacterized protein vp2116; PDBTitle: the crystal structure of the protein with unknown function from vibrio2 parahaemolyticus rimd 2210633
54 | c2pyyB_ |
| not modelled | 20.1 | 21 | PDB header:transport protein Chain: B: PDB Molecule:ionotropic glutamate receptor bacterial homologue; PDBTitle: crystal structure of the glur0 ligand-binding core from nostoc2 punctiforme in complex with (l)-glutamate
55 | c1zypB_ |
| not modelled | 20.0 | 16 | PDB header:oxidoreductase Chain: B: PDB Molecule:alkyl hydroperoxide reductase subunit f; PDBTitle: synchrotron reduced form of the n-terminal domain of2 salmonella typhimurium ahpf
56 | c1wu2B_ |
| not modelled | 19.3 | 29 | PDB header:structural genomics,biosynthetic protein Chain: B: PDB Molecule:molybdopterin biosynthesis moea protein; PDBTitle: crystal structure of molybdopterin biosynthesis moea2 protein from pyrococcus horikoshii ot3
57 | c1w89E_ |
| not modelled | 19.0 | 24 | PDB header:electron transport Chain: E: PDB Molecule:thioredoxin; PDBTitle: structure of the reduced form of human thioredoxin 2
58 | c3h7mA_ |
| not modelled | 18.9 | 15 | PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of a histidine kinase sensor domain with2 similarity to periplasmic binding proteins
59 | c1yvyA_ |
| not modelled | 18.7 | 18 | PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase [atp]; PDBTitle: crystal strucutre of anaerobiospirillum succiniciproducens2 phosphoenolpyruvate carboxykinase
60 | d1thxa_ |
| not modelled | 18.5 | 16 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
61 | d1dbya_ |
| not modelled | 18.4 | 14 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
62 | c1zu4A_ |
| not modelled | 18.3 | 16 | PDB header:protein transport Chain: A: PDB Molecule:ftsy; PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212
63 | c3delC_ |
| not modelled | 18.2 | 11 | PDB header:protein binding, transport protein Chain: C: PDB Molecule:arginine binding protein; PDBTitle: the structure of ct381, the arginine binding protein from the2 periplasm chlamydia trachomatis
64 | c3kzgB_ |
| not modelled | 18.2 | 14 | PDB header:transport protein Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila
65 | d2ftsa2 |
| not modelled | 18.1 | 27 | Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like
66 | c2vhaB_ |
| not modelled | 17.9 | 18 | PDB header:transport protein Chain: B: PDB Molecule:periplasmic binding transport protein; PDBTitle: debp
67 | d1l1fa2 |
| not modelled | 17.8 | 12 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
68 | d1eeja1 |
| not modelled | 17.7 | 32 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbC/DsbG C-terminal domain-like
69 | d1r89a1 |
| not modelled | 17.6 | 12 | Fold:PAP/OAS1 substrate-binding domain Superfamily:PAP/OAS1 substrate-binding domain Family:Archaeal tRNA CCA-adding enzyme substrate-binding domain
70 | d1lsta_ |
| not modelled | 17.5 | 18 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
71 | c2vimA_ |
| not modelled | 17.3 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: x-ray structure of fasciola hepatica thioredoxin
72 | d1hsla_ |
| not modelled | 17.2 | 6 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
73 | c3apsA_ |
| not modelled | 17.2 | 27 | PDB header:oxidoreductase Chain: A: PDB Molecule:dnaj homolog subfamily c member 10; PDBTitle: crystal structure of trx4 domain of erdj5
74 | c2ieeB_ |
| not modelled | 17.2 | 11 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable abc transporter extracellular-binding PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574.
75 | c3tcoA_ |
| not modelled | 17.1 | 16 | PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin (trxa-1); PDBTitle: crystallographic and spectroscopic characterization of sulfolobus2 solfataricus trxa1 provide insights into the determinants of3 thioredoxin fold stability
76 | d2bv3a4 |
| not modelled | 16.6 | 16 | Fold:Ferredoxin-like Superfamily:EF-G C-terminal domain-like Family:EF-G/eEF-2 domains III and V
77 | d2es7a1 |
| not modelled | 16.6 | 21 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:HyaE-like
78 | d1m7ta_ |
| not modelled | 16.6 | 16 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
79 | c1jzdA_ |
| not modelled | 16.5 | 27 | PDB header:oxidoreductase Chain: A: PDB Molecule:thiol:disulfide interchange protein dsbc; PDBTitle: dsbc-dsbdalpha complex
80 | c2oe0B_ |
| not modelled | 16.5 | 16 | PDB header:electron transport Chain: B: PDB Molecule:thioredoxin-3; PDBTitle: crystal structure of mitochondrial thioredoxin 3 from2 saccharomyces cerevisiae
81 | c3kbrA_ |
| not modelled | 16.4 | 22 | PDB header:lyase Chain: A: PDB Molecule:cyclohexadienyl dehydratase; PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01
82 | d2f34a1 |
| not modelled | 16.3 | 12 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
83 | c1t3bA_ |
| not modelled | 15.8 | 19 | PDB header:isomerase Chain: A: PDB Molecule:thiol:disulfide interchange protein dsbc; PDBTitle: x-ray structure of dsbc from haemophilus influenzae
84 | d2cvba1 |
| not modelled | 15.7 | 5 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
85 | c2ylnA_ |
| not modelled | 15.7 | 11 | PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation
86 | d1xwaa_ |
| not modelled | 15.7 | 18 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
87 | d1ep7a_ |
| not modelled | 15.6 | 11 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
88 | c1xbsA_ |
| not modelled | 15.6 | 21 | PDB header:transcription, cell cycle Chain: A: PDB Molecule:dim1-like protein; PDBTitle: crystal structure of human dim2: a dim1-like protein
89 | d1ti3a_ |
| not modelled | 15.5 | 10 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase
90 | d1t3ba1 |
| not modelled | 15.4 | 19 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbC/DsbG C-terminal domain-like
91 | c2xbqB_ |
| not modelled | 15.3 | 18 | PDB header:oxidoreductase Chain: B: PDB Molecule:thioredoxin; PDBTitle: crystal structure of reduced schistosoma mansoni2 thioredoxin pre-protein at 1.7 angstrom
92 | c3hypB_ |
| not modelled | 15.3 | 18 | PDB header:electron transport Chain: B: PDB Molecule:thioredoxin; PDBTitle: crystal structure of bacteroides fragilis trxp_s105g mutant
93 | c3g41A_ |
| not modelled | 15.1 | 22 | PDB header:transport protein Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae
94 | c3kp8A_ |
| not modelled | 15.1 | 21 | PDB header:oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: the thioredoxin-like domain of a vkor homolog from2 synechococcus sp.
95 | c3g9bA_ |
| not modelled | 15.0 | 24 | PDB header:transferase Chain: A: PDB Molecule:dolichyl-diphosphooligosaccharide-protein PDBTitle: crystal structure of reduced ost6l
96 | c2dj1A_ |
| not modelled | 15.0 | 11 | PDB header:isomerase Chain: A: PDB Molecule:protein disulfide-isomerase a4; PDBTitle: the solution structure of the first thioredoxin domain of2 mouse protein disulfide-isomerase a4
97 | c1t00A_ |
| not modelled | 14.8 | 11 | PDB header:electron transport Chain: A: PDB Molecule:thioredoxin; PDBTitle: the structure of thioredoxin from s. coelicolor
98 | d1dd9a_ |
| not modelled | 14.7 | 22 | Fold:DNA primase core Superfamily:DNA primase core Family:DNA primase DnaG catalytic core
99 | c1dd9A_ |
| not modelled | 14.7 | 22 | PDB header:transferase Chain: A: PDB Molecule:dna primase; PDBTitle: structure of the dnag catalytic core

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