Phyre 2 Results for P24205

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Email | l.a.kelley@imperial.ac.uk
Description | P24205
Date | Thu Jan 5 11:41:14 GMT 2012
Unique Job ID | 0755821a9535454d

Summary |

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

Model (left) based on template c1ltxA_
Top template information
PDB header:transferase/protein binding Chain: A: PDB Molecule:rab geranylgeranyltransferase alpha subunit; PDBTitle: structure of rab escort protein-1 in complex with rab2 geranylgeranyl transferase and isoprenoid
Confidence and coverage
Confidence: | 64.7% | Coverage: | 11%
36 residues ( 11% of your sequence) have been modelled with 64.7% confidence by the single highest scoring template.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | E | T | K | K | N | N | S | E | Y | I | P | E | F | D | K | S | F | R | H | P | R | Y | W | G | A | W | L | G | V | A | A | M | A | G | I | A | L | T | P | P | K | F | R | D | P | I | L | A | R | L | G | R | F | A | G | R | L | G | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | S | R | R | R | A | L | I | N | L | S | L | C | F | P | E | R | S | E | A | E | R | E | A | I | V | D | E | M | F | A | T | A | P | Q | A | M | A | M | M | A | E | L | A | I | R | G | P | E | K | I | Q | P | R | V | D | W | Q | G | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | E | I | I | E | E | M | R | R | N | N | E | K | V | I | F | L | V | P | H | G | W | A | V | D | I | P | A | M | L | M | A | S | Q | G | Q | K | M | A | A | M | F | H | N | Q | G | N | P | V | F | D | Y | V | W | N | T | V | R | R | R | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | G | G | R | L | H | A | R | N | D | G | I | K | P | F | I | Q | S | V | R | Q | G | Y | W | G | Y | Y | L | P | D | Q | D | H | G | P | E | H | S | E | F | V | D | F | F | A | T | Y | K | A | T | L | P | A | I | G | R | L | M | K | V | C
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | R | A | R | V | V | P | L | F | P | I | Y | D | G | K | T | H | R | L | T | I | Q | V | R | P | P | M | D | D | L | L | E | A | D | D | H | T | I | A | R | R | M | N | E | E | V | E | I | F | V | G | P | R | P | E | Q | Y | T | W | I | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | .
Sequence |  | K | L | L | K | T | R | K | P | G | E | I | Q | P | Y | K | R | K | D | L | Y | P | I | 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 |
| c1ltxA_ |

### PDB 1ltx chain A

Region: 268 - 303
Aligned: 36
Modelled: 36
Confidence: 64.7%
Identity: 14%
PDB header:transferase/protein binding
Chain: A: PDB Molecule:rab geranylgeranyltransferase alpha subunit;
PDBTitle: structure of rab escort protein-1 in complex with rab2 geranylgeranyl transferase and isoprenoid

Phyre2
2 |
| d1j7ja_ |

### PDB 1j7j chain A

Region: 106 - 227
Aligned: 116
Modelled: 122
Confidence: 55.9%
Identity: 13%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
3 |
| d1kl7a_ |

### PDB 1kl7 chain A

Region: 61 - 200
Aligned: 140
Modelled: 140
Confidence: 55.3%
Identity: 6%
Fold: Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily: Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family: Tryptophan synthase beta subunit-like PLP-dependent enzymes

Phyre2
4 |
| d1g9sa_ |

### PDB 1g9s chain A

Region: 107 - 228
Aligned: 122
Modelled: 122
Confidence: 49.2%
Identity: 12%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
5 |
| c2j5bA_ |

### PDB 2j5b chain A

Region: 116 - 143
Aligned: 28
Modelled: 28
Confidence: 44.6%
Identity: 11%
PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: structure of the tyrosyl trna synthetase from acanthamoeba2 polyphaga mimivirus complexed with tyrosynol

Phyre2
6 |
| d1a3ca_ |

### PDB 1a3c chain A

Region: 183 - 231
Aligned: 48
Modelled: 49
Confidence: 42.3%
Identity: 10%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
7 |
| d2igba1 |

### PDB 2igb chain A domain 1

Region: 183 - 231
Aligned: 48
Modelled: 49
Confidence: 36.0%
Identity: 15%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
8 |
| c1xuzA_ |

### PDB 1xuz chain A

Region: 116 - 245
Aligned: 96
Modelled: 96
Confidence: 34.3%
Identity: 10%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:polysialic acid capsule biosynthesis protein siac;
PDBTitle: crystal structure analysis of sialic acid synthase (neub)from2 neisseria meningitidis, bound to mn2+, phosphoenolpyruvate, and n-3 acetyl mannosaminitol

Phyre2
9 |
| c2pjuD_ |

### PDB 2pju chain D

Region: 125 - 249
Aligned: 104
Modelled: 104
Confidence: 33.9%
Identity: 11%
PDB header:transcription
Chain: D: PDB Molecule:propionate catabolism operon regulatory protein;
PDBTitle: crystal structure of propionate catabolism operon2 regulatory protein prpr

Phyre2
10 |
| c1yfzA_ |

### PDB 1yfz chain A

Region: 129 - 228
Aligned: 100
Modelled: 100
Confidence: 33.9%
Identity: 7%
PDB header:transferase
Chain: A: PDB Molecule:hypoxanthine-guanine phosphoribosyltransferase;
PDBTitle: novel imp binding in feedback inhibition of hypoxanthine-guanine2 phosphoribosyltransferase from thermoanaerobacter tengcongensis

Phyre2
11 |
| d1yfza1 |

### PDB 1yfz chain A domain 1

Region: 129 - 228
Aligned: 100
Modelled: 100
Confidence: 33.9%
Identity: 7%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
12 |
| c3efhB_ |

### PDB 3efh chain B

Region: 120 - 203
Aligned: 83
Modelled: 84
Confidence: 32.2%
Identity: 8%
PDB header:transferase
Chain: B: PDB Molecule:ribose-phosphate pyrophosphokinase 1;
PDBTitle: crystal structure of human phosphoribosyl pyrophosphate2 synthetase 1

Phyre2
13 |
| d1nkta4 |

### PDB 1nkt chain A domain 4

Region: 120 - 194
Aligned: 73
Modelled: 73
Confidence: 31.3%
Identity: 12%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2
14 |
| c3o7mD_ |

### PDB 3o7m chain D

Region: 121 - 228
Aligned: 108
Modelled: 108
Confidence: 31.3%
Identity: 7%
PDB header:transferase
Chain: D: PDB Molecule:hypoxanthine phosphoribosyltransferase;
PDBTitle: 1.98 angstrom resolution crystal structure of a hypoxanthine-guanine2 phosphoribosyltransferase (hpt-2) from bacillus anthracis str. 'ames3 ancestor'

Phyre2
15 |
| d2zdra2 |

### PDB 2zdr chain A domain 2

Region: 117 - 245
Aligned: 95
Modelled: 95
Confidence: 29.0%
Identity: 11%
Fold: TIM beta/alpha-barrel
Superfamily: Aldolase
Family: NeuB-like

Phyre2
16 |
| d1ufra_ |

### PDB 1ufr chain A

Region: 183 - 231
Aligned: 48
Modelled: 49
Confidence: 28.8%
Identity: 13%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
17 |
| c3lubE_ |

### PDB 3lub chain E

Region: 121 - 142
Aligned: 22
Modelled: 22
Confidence: 28.4%
Identity: 23%
PDB header:hydrolase
Chain: E: PDB Molecule:putative creatinine amidohydrolase;
PDBTitle: crystal structure of putative creatinine amidohydrolase2 (yp_211512.1) from bacteroides fragilis nctc 9343 at 2.11 a3 resolution

Phyre2
18 |
| d1v7za_ |

### PDB 1v7z chain A

Region: 120 - 161
Aligned: 42
Modelled: 42
Confidence: 26.8%
Identity: 17%
Fold: Creatininase
Superfamily: Creatininase
Family: Creatininase

Phyre2
19 |
| d1w30a_ |

### PDB 1w30 chain A

Region: 183 - 231
Aligned: 48
Modelled: 49
Confidence: 25.9%
Identity: 15%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
20 |
| c2q5cA_ |

### PDB 2q5c chain A

Region: 125 - 249
Aligned: 104
Modelled: 104
Confidence: 24.3%
Identity: 9%
PDB header:transcription
Chain: A: PDB Molecule:ntrc family transcriptional regulator;
PDBTitle: crystal structure of ntrc family transcriptional regulator from2 clostridium acetobutylicum

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1ltxA_ |
|  | 64.7 | 14 | PDB header:transferase/protein binding Chain: A: PDB Molecule:rab geranylgeranyltransferase alpha subunit; PDBTitle: structure of rab escort protein-1 in complex with rab2 geranylgeranyl transferase and isoprenoid
2 | d1j7ja_ |
|  | 55.9 | 13 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
3 | d1kl7a_ |
|  | 55.3 | 6 | Fold:Tryptophan synthase beta subunit-like PLP-dependent enzymes Superfamily:Tryptophan synthase beta subunit-like PLP-dependent enzymes Family:Tryptophan synthase beta subunit-like PLP-dependent enzymes
4 | d1g9sa_ |
|  | 49.2 | 12 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
5 | c2j5bA_ |
|  | 44.6 | 11 | PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: structure of the tyrosyl trna synthetase from acanthamoeba2 polyphaga mimivirus complexed with tyrosynol
6 | d1a3ca_ |
|  | 42.3 | 10 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
7 | d2igba1 |
|  | 36.0 | 15 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
8 | c1xuzA_ |
|  | 34.3 | 10 | PDB header:biosynthetic protein Chain: A: PDB Molecule:polysialic acid capsule biosynthesis protein siac; PDBTitle: crystal structure analysis of sialic acid synthase (neub)from2 neisseria meningitidis, bound to mn2+, phosphoenolpyruvate, and n-3 acetyl mannosaminitol
9 | c2pjuD_ |
|  | 33.9 | 11 | PDB header:transcription Chain: D: PDB Molecule:propionate catabolism operon regulatory protein; PDBTitle: crystal structure of propionate catabolism operon2 regulatory protein prpr
10 | c1yfzA_ |
|  | 33.9 | 7 | PDB header:transferase Chain: A: PDB Molecule:hypoxanthine-guanine phosphoribosyltransferase; PDBTitle: novel imp binding in feedback inhibition of hypoxanthine-guanine2 phosphoribosyltransferase from thermoanaerobacter tengcongensis
11 | d1yfza1 |
|  | 33.9 | 7 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
12 | c3efhB_ |
|  | 32.2 | 8 | PDB header:transferase Chain: B: PDB Molecule:ribose-phosphate pyrophosphokinase 1; PDBTitle: crystal structure of human phosphoribosyl pyrophosphate2 synthetase 1
13 | d1nkta4 |
|  | 31.3 | 12 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Tandem AAA-ATPase domain
14 | c3o7mD_ |
|  | 31.3 | 7 | PDB header:transferase Chain: D: PDB Molecule:hypoxanthine phosphoribosyltransferase; PDBTitle: 1.98 angstrom resolution crystal structure of a hypoxanthine-guanine2 phosphoribosyltransferase (hpt-2) from bacillus anthracis str. 'ames3 ancestor'
15 | d2zdra2 |
|  | 29.0 | 11 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:NeuB-like
16 | d1ufra_ |
|  | 28.8 | 13 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
17 | c3lubE_ |
|  | 28.4 | 23 | PDB header:hydrolase Chain: E: PDB Molecule:putative creatinine amidohydrolase; PDBTitle: crystal structure of putative creatinine amidohydrolase2 (yp_211512.1) from bacteroides fragilis nctc 9343 at 2.11 a3 resolution
18 | d1v7za_ |
|  | 26.8 | 17 | Fold:Creatininase Superfamily:Creatininase Family:Creatininase
19 | d1w30a_ |
|  | 25.9 | 15 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
20 | c2q5cA_ |
|  | 24.3 | 9 | PDB header:transcription Chain: A: PDB Molecule:ntrc family transcriptional regulator; PDBTitle: crystal structure of ntrc family transcriptional regulator from2 clostridium acetobutylicum
21 | c3cwcB_ |
| not modelled | 24.1 | 8 | PDB header:transferase Chain: B: PDB Molecule:putative glycerate kinase 2; PDBTitle: crystal structure of putative glycerate kinase 2 from salmonella2 typhimurium lt2
22 | c3no4A_ |
| not modelled | 24.0 | 12 | PDB header:hydrolase Chain: A: PDB Molecule:creatinine amidohydrolase; PDBTitle: crystal structure of a creatinine amidohydrolase (npun_f1913) from2 nostoc punctiforme pcc 73102 at 2.00 a resolution
23 | d1d8da_ |
| not modelled | 22.4 | 14 | Fold:alpha-alpha superhelix Superfamily:Protein prenylyltransferase Family:Protein prenylyltransferase
24 | d1hgxa_ |
| not modelled | 22.4 | 11 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
25 | d1pzma_ |
| not modelled | 21.0 | 11 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
26 | d1l1qa_ |
| not modelled | 19.1 | 8 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
27 | d1wgla_ |
| not modelled | 18.6 | 11 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain
28 | c2ps3A_ |
| not modelled | 18.4 | 12 | PDB header:metal transport Chain: A: PDB Molecule:high-affinity zinc uptake system protein znua; PDBTitle: structure and metal binding properties of znua, a2 periplasmic zinc transporter from escherichia coli
29 | d1a9xb1 |
| not modelled | 17.6 | 15 | Fold:The "swivelling" beta/beta/alpha domain Superfamily:Carbamoyl phosphate synthetase, small subunit N-terminal domain Family:Carbamoyl phosphate synthetase, small subunit N-terminal domain
30 | c2dhyA_ |
| not modelled | 17.6 | 10 | PDB header:immune system Chain: A: PDB Molecule:cue domain-containing protein 1; PDBTitle: solution structure of the cue domain in the human cue2 domain containing protein 1 (cuedc1)
31 | c2ov3A_ |
| not modelled | 17.3 | 17 | PDB header:transport protein Chain: A: PDB Molecule:periplasmic binding protein component of an abc PDBTitle: crystal structure of 138-173 znua deletion mutant plus zinc2 bound
32 | d1o60a_ |
| not modelled | 17.1 | 11 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I DAHP synthetase
33 | c3kb8A_ |
| not modelled | 17.0 | 9 | PDB header:transferase Chain: A: PDB Molecule:hypoxanthine phosphoribosyltransferase; PDBTitle: 2.09 angstrom resolution structure of a hypoxanthine-guanine2 phosphoribosyltransferase (hpt-1) from bacillus anthracis str. 'ames3 ancestor' in complex with gmp
34 | d1hrua_ |
| not modelled | 16.4 | 20 | Fold:YrdC/RibB Superfamily:YrdC/RibB Family:YrdC-like
35 | c2ywtA_ |
| not modelled | 16.1 | 7 | PDB header:transferase Chain: A: PDB Molecule:hypoxanthine-guanine phosphoribosyltransferase; PDBTitle: crystal structure of hypoxanthine-guanine2 phosphoribosyltransferase with gmp from thermus3 thermophilus hb8
36 | d1d7ya2 |
| not modelled | 15.7 | 8 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains
37 | c2o1eB_ |
| not modelled | 15.4 | 10 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:ycdh; PDBTitle: crystal structure of the metal-dependent lipoprotein ycdh2 from bacillus subtilis, northeast structural genomics3 target sr583
38 | d1jcua_ |
| not modelled | 15.3 | 21 | Fold:YrdC/RibB Superfamily:YrdC/RibB Family:YrdC-like
39 | d2h6fa1 |
| not modelled | 15.3 | 14 | Fold:alpha-alpha superhelix Superfamily:Protein prenylyltransferase Family:Protein prenylyltransferase
40 | d1cv8a_ |
| not modelled | 15.2 | 11 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Papain-like
41 | d1gm5a4 |
| not modelled | 15.2 | 10 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Tandem AAA-ATPase domain
42 | c3f6tA_ |
| not modelled | 15.1 | 15 | PDB header:transferase Chain: A: PDB Molecule:aspartate aminotransferase; PDBTitle: crystal structure of aspartate aminotransferase (e.c. 2.6.1.1)2 (yp_194538.1) from lactobacillus acidophilus ncfm at 2.15 a3 resolution
43 | c3dl8B_ |
| not modelled | 14.9 | 11 | PDB header:protein transport Chain: B: PDB Molecule:protein translocase subunit seca; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca
44 | c2cycB_ |
| not modelled | 14.3 | 7 | PDB header:ligase Chain: B: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of tyrosyl-trna synthetase complexed with l-tyrosine2 from pyrococcus horikoshii
45 | d2obba1 |
| not modelled | 14.1 | 12 | Fold:HAD-like Superfamily:HAD-like Family:BT0820-like
46 | d1k7ja_ |
| not modelled | 13.9 | 25 | Fold:YrdC/RibB Superfamily:YrdC/RibB Family:YrdC-like
47 | c1keeH_ |
| not modelled | 13.5 | 15 | PDB header:ligase Chain: H: PDB Molecule:carbamoyl-phosphate synthetase small chain; PDBTitle: inactivation of the amidotransferase activity of carbamoyl phosphate2 synthetase by the antibiotic acivicin
48 | c3mioA_ |
| not modelled | 13.3 | 16 | PDB header:lyase Chain: A: PDB Molecule:3,4-dihydroxy-2-butanone 4-phosphate synthase; PDBTitle: crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase2 domain from mycobacterium tuberculosis at ph 6.00
49 | d1tksa_ |
| not modelled | 13.3 | 14 | Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
50 | c1tnoI_ |
| not modelled | 13.2 | 12 | PDB header:transferase Chain: I: PDB Molecule:geranylgeranyltransferase type i alpha subunit; PDBTitle: rat protein geranylgeranyltransferase type-i complexed with2 a ggpp analog and a kkksktkcvim peptide derived from k-3 ras4b
51 | c2advB_ |
| not modelled | 13.0 | 23 | PDB header:hydrolase Chain: B: PDB Molecule:glutaryl 7- aminocephalosporanic acid acylase; PDBTitle: crystal structures of glutaryl 7-aminocephalosporanic acid acylase:2 mutational study of activation mechanism
52 | d1tuwa_ |
| not modelled | 12.9 | 22 | Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Polyketide synthesis cyclase
53 | d1p3qq_ |
| not modelled | 12.7 | 17 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain
54 | d1snna_ |
| not modelled | 12.5 | 13 | Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
55 | d1xdfa1 |
| not modelled | 12.5 | 18 | Fold:TBP-like Superfamily:Bet v1-like Family:Pathogenesis-related protein 10 (PR10)-like
56 | c3m8yC_ |
| not modelled | 12.4 | 11 | PDB header:isomerase Chain: C: PDB Molecule:phosphopentomutase; PDBTitle: phosphopentomutase from bacillus cereus after glucose-1,6-bisphosphate2 activation
57 | c1tf2A_ |
| not modelled | 12.4 | 11 | PDB header:protein transport Chain: A: PDB Molecule:preprotein translocase seca subunit; PDBTitle: crystal structure of seca:adp in an open conformation from2 bacillus subtilis
58 | c1fcuA_ |
| not modelled | 12.4 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase
59 | d1mn3a_ |
| not modelled | 12.2 | 18 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain
60 | d1fl2a2 |
| not modelled | 12.1 | 9 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains
61 | d1fcqa_ |
| not modelled | 11.8 | 11 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Bee venom hyaluronidase
62 | c1pzmB_ |
| not modelled | 11.7 | 11 | PDB header:transferase Chain: B: PDB Molecule:hypoxanthine-guanine phosphoribosyltransferase; PDBTitle: crystal structure of hgprt-ase from leishmania tarentolae in complex2 with gmp
63 | d1tc1a_ |
| not modelled | 11.5 | 9 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
64 | d2pjua1 |
| not modelled | 11.4 | 11 | Fold:Chelatase-like Superfamily:PrpR receptor domain-like Family:PrpR receptor domain-like
65 | d1pyfa_ |
| not modelled | 11.2 | 8 | Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP)
66 | d1iuqa_ |
| not modelled | 11.1 | 22 | Fold:Glycerol-3-phosphate (1)-acyltransferase Superfamily:Glycerol-3-phosphate (1)-acyltransferase Family:Glycerol-3-phosphate (1)-acyltransferase
67 | d1g2qa_ |
| not modelled | 10.9 | 10 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
68 | c2h3oA_ |
| not modelled | 10.7 | 9 | PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices
69 | d3pmga2 |
| not modelled | 10.5 | 8 | Fold:Phosphoglucomutase, first 3 domains Superfamily:Phosphoglucomutase, first 3 domains Family:Phosphoglucomutase, first 3 domains
70 | c2ns6A_ |
| not modelled | 10.3 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:mobilization protein a; PDBTitle: crystal structure of the minimal relaxase domain of moba2 from plasmid r1162
71 | d1ikpa3 |
| not modelled | 10.3 | 27 | Fold:Toxins' membrane translocation domains Superfamily:Exotoxin A, middle domain Family:Exotoxin A, middle domain
72 | d1v71a1 |
| not modelled | 9.9 | 11 | Fold:Tryptophan synthase beta subunit-like PLP-dependent enzymes Superfamily:Tryptophan synthase beta subunit-like PLP-dependent enzymes Family:Tryptophan synthase beta subunit-like PLP-dependent enzymes
73 | c2pe4A_ |
| not modelled | 9.7 | 21 | PDB header:hydrolase Chain: A: PDB Molecule:hyaluronidase-1; PDBTitle: structure of human hyaluronidase 1, a hyaluronan hydrolyzing enzyme2 involved in tumor growth and angiogenesis
74 | d2pw6a1 |
| not modelled | 9.7 | 7 | Fold:Phosphorylase/hydrolase-like Superfamily:LigB-like Family:LigB-like
75 | d1xrsa_ |
| not modelled | 9.6 | 19 | Fold:TIM beta/alpha-barrel Superfamily:Cobalamin (vitamin B12)-dependent enzymes Family:D-lysine 5,6-aminomutase alpha subunit, KamD
76 | c3ktsA_ |
| not modelled | 9.6 | 12 | PDB header:transcriptional regulator Chain: A: PDB Molecule:glycerol uptake operon antiterminator regulatory protein; PDBTitle: crystal structure of glycerol uptake operon antiterminator regulatory2 protein from listeria monocytogenes str. 4b f2365
77 | d1iyjb4 |
| not modelled | 9.5 | 33 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB
78 | c3iraA_ |
| not modelled | 9.3 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein; PDBTitle: the crystal structure of one domain of the conserved protein from2 methanosarcina mazei go1
79 | d1nj1a2 |
| not modelled | 9.1 | 13 | Fold:IF3-like Superfamily:C-terminal domain of ProRS Family:C-terminal domain of ProRS
80 | d2aeea1 |
| not modelled | 8.8 | 4 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
81 | c2lc0A_ |
| not modelled | 8.8 | 10 | PDB header:protein binding Chain: A: PDB Molecule:putative uncharacterized protein tb39.8; PDBTitle: rv0020c_nter structure
82 | d2pi8a1 |
| not modelled | 8.7 | 11 | Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like
83 | d1vzya2 |
| not modelled | 8.6 | 17 | Fold:HSP33 redox switch-like Superfamily:HSP33 redox switch-like Family:HSP33 redox switch-like
84 | d1mkya3 |
| not modelled | 8.6 | 6 | Fold:Alpha-lytic protease prodomain-like Superfamily:Probable GTPase Der, C-terminal domain Family:Probable GTPase Der, C-terminal domain
85 | d1k4ia_ |
| not modelled | 8.5 | 16 | Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
86 | c2qx5B_ |
| not modelled | 8.2 | 29 | PDB header:transport protein Chain: B: PDB Molecule:nucleoporin nic96; PDBTitle: structure of nucleoporin nic96
87 | c3dezA_ |
| not modelled | 8.2 | 8 | PDB header:transferase Chain: A: PDB Molecule:orotate phosphoribosyltransferase; PDBTitle: crystal structure of orotate phosphoribosyltransferase from2 streptococcus mutans
88 | c2eqaA_ |
| not modelled | 8.0 | 21 | PDB header:rna binding protein Chain: A: PDB Molecule:hypothetical protein st1526; PDBTitle: crystal structure of the hypothetical sua5 protein from2 sulfolobus tokodaii
89 | c2jcyA_ |
| not modelled | 7.9 | 14 | PDB header:oxidoreductase Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis
90 | c3koxA_ |
| not modelled | 7.8 | 16 | PDB header:metal binding protein Chain: A: PDB Molecule:d-ornithine aminomutase e component; PDBTitle: crystal structure of ornithine 4,5 aminomutase in complex with 2,4-2 diaminobutyrate (anaerobic)
91 | c3cx3A_ |
| not modelled | 7.8 | 11 | PDB header:metal binding protein Chain: A: PDB Molecule:lipoprotein; PDBTitle: crystal structure analysis of the streptococcus pneumoniae2 adcaii protein
92 | c3khsB_ |
| not modelled | 7.7 | 11 | PDB header:hydrolase Chain: B: PDB Molecule:purine nucleoside phosphorylase; PDBTitle: crystal structure of grouper iridovirus purine nucleoside2 phosphorylase
93 | c1r6uB_ |
| not modelled | 7.6 | 8 | PDB header:ligase Chain: B: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: crystal structure of an active fragment of human tryptophanyl-trna2 synthetase with cytokine activity
94 | d1nj8a2 |
| not modelled | 7.6 | 17 | Fold:IF3-like Superfamily:C-terminal domain of ProRS Family:C-terminal domain of ProRS
95 | c2bnlE_ |
| not modelled | 7.5 | 12 | PDB header:stress-response Chain: E: PDB Molecule:modulator protein rsbr; PDBTitle: the structure of the n-terminal domain of rsbr
96 | c3g8rA_ |
| not modelled | 7.4 | 12 | PDB header:biosynthetic protein Chain: A: PDB Molecule:probable spore coat polysaccharide biosynthesis protein e; PDBTitle: crystal structure of putative spore coat polysaccharide biosynthesis2 protein e from chromobacterium violaceum atcc 12472
97 | c3l6gA_ |
| not modelled | 7.4 | 12 | PDB header:glycine betaine-binding protein Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding PDBTitle: crystal structure of lactococcal opuac in its open conformation
98 | d1p17b_ |
| not modelled | 7.4 | 9 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
99 | c3ie5A_ |
| not modelled | 7.3 | 20 | PDB header:plant protein, biosynthetic protein Chain: A: PDB Molecule:phenolic oxidative coupling protein hyp-1; PDBTitle: crystal structure of hyp-1 protein from hypericum perforatum2 (st john's wort) involved in hypericin biosynthesis

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