Phyre 2 Results for P0AE01

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Email | l.a.kelley@imperial.ac.uk
Description | P0AE01
Date | Thu Jan 5 11:22:11 GMT 2012
Unique Job ID | 15305cd3482d4b50

Summary |

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

Model (left) based on template c3ilkB_
Top template information
PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized trna/rrna methyltransferase hi0380; PDBTitle: the structure of a probable methylase family protein from haemophilus2 influenzae rd kw20
Confidence and coverage
Confidence: | 100.0% | Coverage: | 95%
233 residues ( 95% 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 | L | Q | N | I | R | I | V | L | V | E | T | S | H | T | G | N | M | G | S | V | A | R | A | M | K | T | M | G | L | T | N | L | W | L | V | N | P | L | V | K | P | D | S | Q | A | I | A | L | A | A | G | A | S | D | V | I | G | N | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | H | I | V | D | T | L | D | E | A | L | A | G | C | S | L | V | V | G | T | S | A | R | S | R | T | L | P | W | P | M | L | D | P | R | E | C | G | L | K | S | V | A | E | A | A | N | T | P | V | A | L | V | F | G | R | E | R | V | G | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | T | N | E | E | L | Q | K | C | H | Y | H | V | A | I | A | A | N | P | E | Y | S | S | L | N | L | A | M | A | V | Q | V | I | A | Y | E | V | R | M | A | W | L | A | T | Q | E | N | G | E | Q | V | E | H | E | E | T | P | Y | P | L | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | D | D | L | E | R | F | Y | G | H | L | E | Q | T | L | L | A | T | G | F | I | R | E | N | H | P | G | Q | V | M | N | K | L | R | R | L | F | T | R | A | R | P | E | S | Q | E | L | N | I | L | R | G | I | L | A | S | I | E | Q | Q | N
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | .
Sequence |  | K | G | N | K | A | E
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 |
| c3ilkB_ |

### PDB 3ilk chain B

Region: 1 - 244
Aligned: 233
Modelled: 226
Confidence: 100.0%
Identity: 54%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized trna/rrna methyltransferase hi0380;
PDBTitle: the structure of a probable methylase family protein from haemophilus2 influenzae rd kw20

Phyre2
2 |
| c3ic6A_ |

### PDB 3ic6 chain A

Region: 2 - 193
Aligned: 185
Modelled: 191
Confidence: 100.0%
Identity: 41%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative methylase family protein;
PDBTitle: crystal structure of putative methylase family protein from neisseria2 gonorrhoeae

Phyre2
3 |
| c3onpA_ |

### PDB 3onp chain A

Region: 4 - 159
Aligned: 156
Modelled: 151
Confidence: 100.0%
Identity: 35%
PDB header:transferase
Chain: A: PDB Molecule:trna/rrna methyltransferase (spou);
PDBTitle: crystal structure of trna/rrna methyltransferase spou from rhodobacter2 sphaeroides

Phyre2
4 |
| c1zjrA_ |

### PDB 1zjr chain A

Region: 3 - 190
Aligned: 172
Modelled: 172
Confidence: 100.0%
Identity: 16%
PDB header:transferase
Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase;
PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme

Phyre2
5 |
| c3ktyA_ |

### PDB 3kty chain A

Region: 2 - 161
Aligned: 157
Modelled: 155
Confidence: 100.0%
Identity: 41%
PDB header:transferase
Chain: A: PDB Molecule:probable methyltransferase;
PDBTitle: crystal structure of probable methyltransferase from bordetella2 pertussis tohama i

Phyre2
6 |
| d1v2xa_ |

### PDB 1v2x chain A

Region: 3 - 190
Aligned: 171
Modelled: 171
Confidence: 100.0%
Identity: 19%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
7 |
| c2ha8A_ |

### PDB 2ha8 chain A

Region: 3 - 161
Aligned: 151
Modelled: 151
Confidence: 100.0%
Identity: 17%
PDB header:rna binding protein
Chain: A: PDB Molecule:tar (hiv-1) rna loop binding protein;
PDBTitle: methyltransferase domain of human tar (hiv-1) rna binding2 protein 1

Phyre2
8 |
| d1gz0a1 |

### PDB 1gz0 chain A domain 1

Region: 3 - 160
Aligned: 148
Modelled: 158
Confidence: 100.0%
Identity: 19%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
9 |
| c1gz0G_ |

### PDB 1gz0 chain G

Region: 3 - 160
Aligned: 148
Modelled: 148
Confidence: 100.0%
Identity: 19%
PDB header:transferase
Chain: G: PDB Molecule:hypothetical trna/rrna methyltransferase yjfh;
PDBTitle: 23s ribosomal rna g2251 2'o-methyltransferase rlmb

Phyre2
10 |
| c1ipaA_ |

### PDB 1ipa chain A

Region: 3 - 161
Aligned: 148
Modelled: 148
Confidence: 100.0%
Identity: 22%
PDB header:transferase
Chain: A: PDB Molecule:rna 2'-o-ribose methyltransferase;
PDBTitle: crystal structure of rna 2'-o ribose methyltransferase

Phyre2
11 |
| c3dcmX_ |

### PDB 3dcm chain X

Region: 1 - 157
Aligned: 156
Modelled: 156
Confidence: 100.0%
Identity: 17%
PDB header:transferase
Chain: X: PDB Molecule:uncharacterized protein tm_1570;
PDBTitle: crystal structure of the thermotoga maritima spout family2 rna-methyltransferase protein tm1570 in complex with s-3 adenosyl-l-methionine

Phyre2
12 |
| c1x7pB_ |

### PDB 1x7p chain B

Region: 3 - 163
Aligned: 154
Modelled: 154
Confidence: 100.0%
Identity: 19%
PDB header:transferase
Chain: B: PDB Molecule:rrna methyltransferase;
PDBTitle: crystal structure of the spou methyltransferase avirb from2 streptomyces viridochromogenes in complex with the cofactor adomet

Phyre2
13 |
| d1ipaa1 |

### PDB 1ipa chain A domain 1

Region: 3 - 161
Aligned: 148
Modelled: 148
Confidence: 100.0%
Identity: 21%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
14 |
| c2i6dA_ |

### PDB 2i6d chain A

Region: 3 - 159
Aligned: 148
Modelled: 147
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: A: PDB Molecule:rna methyltransferase, trmh family;
PDBTitle: the structure of a putative rna methyltransferase of the trmh family2 from porphyromonas gingivalis.

Phyre2
15 |
| d1mxia_ |

### PDB 1mxi chain A

Region: 5 - 160
Aligned: 145
Modelled: 155
Confidence: 100.0%
Identity: 18%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
16 |
| c3gyqB_ |

### PDB 3gyq chain B

Region: 3 - 163
Aligned: 151
Modelled: 151
Confidence: 100.0%
Identity: 20%
PDB header:transferase
Chain: B: PDB Molecule:rrna (adenosine-2'-o-)-methyltransferase;
PDBTitle: structure of the thiostrepton-resistance methyltransferase2 s-adenosyl-l-methionine complex

Phyre2
17 |
| c3l8uA_ |

### PDB 3l8u chain A

Region: 2 - 160
Aligned: 141
Modelled: 141
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: A: PDB Molecule:putative rrna methylase;
PDBTitle: crystal structure of smu.1707c, a putative rrna methyltransferase from2 streptococcus mutans ua159

Phyre2
18 |
| c3e5yB_ |

### PDB 3e5y chain B

Region: 5 - 160
Aligned: 132
Modelled: 132
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: B: PDB Molecule:trmh family rna methyltransferase;
PDBTitle: crystal structure of trmh family rna methyltransferase from2 burkholderia pseudomallei

Phyre2
19 |
| c1vhkA_ |

### PDB 1vhk chain A

Region: 4 - 156
Aligned: 142
Modelled: 153
Confidence: 95.7%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yqeu;
PDBTitle: crystal structure of an hypothetical protein

Phyre2
20 |
| d1vhka2 |

### PDB 1vhk chain A domain 2

Region: 4 - 157
Aligned: 143
Modelled: 154
Confidence: 95.2%
Identity: 11%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: YggJ C-terminal domain-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3ilkB_ |
|  | 100.0 | 54 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized trna/rrna methyltransferase hi0380; PDBTitle: the structure of a probable methylase family protein from haemophilus2 influenzae rd kw20
2 | c3ic6A_ |
|  | 100.0 | 41 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative methylase family protein; PDBTitle: crystal structure of putative methylase family protein from neisseria2 gonorrhoeae
3 | c3onpA_ |
|  | 100.0 | 35 | PDB header:transferase Chain: A: PDB Molecule:trna/rrna methyltransferase (spou); PDBTitle: crystal structure of trna/rrna methyltransferase spou from rhodobacter2 sphaeroides
4 | c1zjrA_ |
|  | 100.0 | 16 | PDB header:transferase Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase; PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme
5 | c3ktyA_ |
|  | 100.0 | 41 | PDB header:transferase Chain: A: PDB Molecule:probable methyltransferase; PDBTitle: crystal structure of probable methyltransferase from bordetella2 pertussis tohama i
6 | d1v2xa_ |
|  | 100.0 | 19 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
7 | c2ha8A_ |
|  | 100.0 | 17 | PDB header:rna binding protein Chain: A: PDB Molecule:tar (hiv-1) rna loop binding protein; PDBTitle: methyltransferase domain of human tar (hiv-1) rna binding2 protein 1
8 | d1gz0a1 |
|  | 100.0 | 19 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
9 | c1gz0G_ |
|  | 100.0 | 19 | PDB header:transferase Chain: G: PDB Molecule:hypothetical trna/rrna methyltransferase yjfh; PDBTitle: 23s ribosomal rna g2251 2'o-methyltransferase rlmb
10 | c1ipaA_ |
|  | 100.0 | 22 | PDB header:transferase Chain: A: PDB Molecule:rna 2'-o-ribose methyltransferase; PDBTitle: crystal structure of rna 2'-o ribose methyltransferase
11 | c3dcmX_ |
|  | 100.0 | 17 | PDB header:transferase Chain: X: PDB Molecule:uncharacterized protein tm_1570; PDBTitle: crystal structure of the thermotoga maritima spout family2 rna-methyltransferase protein tm1570 in complex with s-3 adenosyl-l-methionine
12 | c1x7pB_ |
|  | 100.0 | 19 | PDB header:transferase Chain: B: PDB Molecule:rrna methyltransferase; PDBTitle: crystal structure of the spou methyltransferase avirb from2 streptomyces viridochromogenes in complex with the cofactor adomet
13 | d1ipaa1 |
|  | 100.0 | 21 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
14 | c2i6dA_ |
|  | 100.0 | 21 | PDB header:transferase Chain: A: PDB Molecule:rna methyltransferase, trmh family; PDBTitle: the structure of a putative rna methyltransferase of the trmh family2 from porphyromonas gingivalis.
15 | d1mxia_ |
|  | 100.0 | 18 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
16 | c3gyqB_ |
|  | 100.0 | 20 | PDB header:transferase Chain: B: PDB Molecule:rrna (adenosine-2'-o-)-methyltransferase; PDBTitle: structure of the thiostrepton-resistance methyltransferase2 s-adenosyl-l-methionine complex
17 | c3l8uA_ |
|  | 100.0 | 24 | PDB header:transferase Chain: A: PDB Molecule:putative rrna methylase; PDBTitle: crystal structure of smu.1707c, a putative rrna methyltransferase from2 streptococcus mutans ua159
18 | c3e5yB_ |
|  | 100.0 | 24 | PDB header:transferase Chain: B: PDB Molecule:trmh family rna methyltransferase; PDBTitle: crystal structure of trmh family rna methyltransferase from2 burkholderia pseudomallei
19 | c1vhkA_ |
|  | 95.7 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein yqeu; PDBTitle: crystal structure of an hypothetical protein
20 | d1vhka2 |
|  | 95.2 | 11 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YggJ C-terminal domain-like
21 | d1duvg2 |
| not modelled | 95.0 | 18 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
22 | c2egwB_ |
| not modelled | 94.9 | 17 | PDB header:rna methyltransferase Chain: B: PDB Molecule:upf0088 protein aq_165; PDBTitle: crystal structure of rrna methyltransferase with sah ligand
23 | d1pvva2 |
| not modelled | 94.8 | 19 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
24 | d1otha2 |
| not modelled | 94.7 | 18 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
25 | d1dxha2 |
| not modelled | 94.3 | 17 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
26 | d1vlva2 |
| not modelled | 93.9 | 26 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
27 | c2w37A_ |
| not modelled | 93.7 | 23 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase, catabolic; PDBTitle: crystal structure of the hexameric catabolic ornithine2 transcarbamylase from lactobacillus hilgardii
28 | d1ml4a2 |
| not modelled | 93.7 | 16 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
29 | c1a1sA_ |
| not modelled | 93.7 | 19 | PDB header:transcarbamylase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: ornithine carbamoyltransferase from pyrococcus furiosus
30 | d1nxza2 |
| not modelled | 93.6 | 12 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YggJ C-terminal domain-like
31 | c1vhyB_ |
| not modelled | 93.5 | 11 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein hi0303; PDBTitle: crystal structure of haemophilus influenzae protein hi0303, pfam2 duf558
32 | d1ekxa2 |
| not modelled | 92.9 | 15 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
33 | c2otcA_ |
| not modelled | 92.5 | 19 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: ornithine transcarbamoylase complexed with n-2 (phosphonacetyl)-l-ornithine
34 | d1v6za2 |
| not modelled | 92.4 | 14 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YggJ C-terminal domain-like
35 | c3updA_ |
| not modelled | 92.2 | 21 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: 2.9 angstrom crystal structure of ornithine carbamoyltransferase2 (argf) from vibrio vulnificus
36 | c1vlvA_ |
| not modelled | 92.2 | 24 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: crystal structure of ornithine carbamoyltransferase (tm1097) from2 thermotoga maritima at 2.25 a resolution
37 | c2p2gD_ |
| not modelled | 92.0 | 23 | PDB header:transferase Chain: D: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: crystal structure of ornithine carbamoyltransferase from mycobacterium2 tuberculosis (rv1656): orthorhombic form
38 | c1ortD_ |
| not modelled | 91.5 | 16 | PDB header:transferase Chain: D: PDB Molecule:ornithine transcarbamoylase; PDBTitle: ornithine transcarbamoylase from pseudomonas aeruginosa
39 | d1pg5a2 |
| not modelled | 91.3 | 12 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
40 | d1tuga1 |
| not modelled | 90.0 | 13 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
41 | c3d6nB_ |
| not modelled | 90.0 | 13 | PDB header:hydrolase/transferase Chain: B: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: crystal structure of aquifex dihydroorotase activated by aspartate2 transcarbamoylase
42 | c3kw2A_ |
| not modelled | 89.7 | 11 | PDB header:transferase Chain: A: PDB Molecule:probable r-rna methyltransferase; PDBTitle: crystal structure of probable rrna-methyltransferase from2 porphyromonas gingivalis
43 | c1fvoB_ |
| not modelled | 89.6 | 19 | PDB header:transferase Chain: B: PDB Molecule:ornithine transcarbamylase; PDBTitle: crystal structure of human ornithine transcarbamylase complexed with2 carbamoyl phosphate
44 | c2cx8B_ |
| not modelled | 89.5 | 15 | PDB header:transferase Chain: B: PDB Molecule:methyl transferase; PDBTitle: crystal structure of methyltransferase with ligand(sah)
45 | c2yy8B_ |
| not modelled | 89.1 | 16 | PDB header:transferase Chain: B: PDB Molecule:upf0106 protein ph0461; PDBTitle: crystal structure of archaeal trna-methylase for position2 56 (atrm56) from pyrococcus horikoshii, complexed with s-3 adenosyl-l-methionine
46 | c1pg5A_ |
| not modelled | 88.9 | 12 | PDB header:transferase Chain: A: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: crystal structure of the unligated (t-state) aspartate2 transcarbamoylase from the extremely thermophilic archaeon sulfolobus3 acidocaldarius
47 | c2rgwD_ |
| not modelled | 88.6 | 19 | PDB header:transferase Chain: D: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: catalytic subunit of m. jannaschii aspartate2 transcarbamoylase
48 | d1js1x2 |
| not modelled | 87.1 | 22 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
49 | c3grfA_ |
| not modelled | 85.3 | 22 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: x-ray structure of ornithine transcarbamoylase from giardia2 lamblia
50 | c1ml4A_ |
| not modelled | 85.2 | 15 | PDB header:transferase Chain: A: PDB Molecule:aspartate transcarbamoylase; PDBTitle: the pala-liganded aspartate transcarbamoylase catalytic subunit from2 pyrococcus abyssi
51 | d2o3aa1 |
| not modelled | 83.8 | 18 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:AF0751-like
52 | c3q98A_ |
| not modelled | 82.8 | 17 | PDB header:transferase Chain: A: PDB Molecule:transcarbamylase; PDBTitle: structure of ygew encoded protein from e. coli
53 | c3gd5D_ |
| not modelled | 82.8 | 21 | PDB header:transferase Chain: D: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: crystal structure of ornithine carbamoyltransferase from gloeobacter2 violaceus
54 | c2ef0A_ |
| not modelled | 82.6 | 23 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: crystal structure of ornithine carbamoyltransferase from thermus2 thermophilus
55 | d2at2a2 |
| not modelled | 79.8 | 14 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
56 | c3n7uD_ |
| not modelled | 74.1 | 31 | PDB header:oxidoreductase Chain: D: PDB Molecule:formate dehydrogenase; PDBTitle: nad-dependent formate dehydrogenase from higher-plant arabidopsis2 thaliana in complex with nad and azide
57 | c3sdsA_ |
| not modelled | 72.6 | 21 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase, mitochondrial; PDBTitle: crystal structure of a mitochondrial ornithine carbamoyltransferase2 from coccidioides immitis
58 | c3lxmC_ |
| not modelled | 72.2 | 16 | PDB header:transferase Chain: C: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: 2.00 angstrom resolution crystal structure of a catalytic2 subunit of an aspartate carbamoyltransferase (pyrb) from3 yersinia pestis co92
59 | d2naca1 |
| not modelled | 72.1 | 23 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
60 | c1js1Z_ |
| not modelled | 71.9 | 22 | PDB header:transferase Chain: Z: PDB Molecule:transcarbamylase; PDBTitle: crystal structure of a new transcarbamylase from the2 anaerobic bacterium bacteroides fragilis at 2.0 a3 resolution
61 | d2qmma1 |
| not modelled | 71.7 | 18 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:AF1056-like
62 | c1zq2A_ |
| not modelled | 70.5 | 26 | PDB header:transferase Chain: A: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: crystal structure of n-acetyl-l-ornithine transcarbamylase2 complexed with cp
63 | c3gg9C_ |
| not modelled | 69.2 | 14 | PDB header:oxidoreductase Chain: C: PDB Molecule:d-3-phosphoglycerate dehydrogenase oxidoreductase protein; PDBTitle: crystal structure of putative d-3-phosphoglycerate dehydrogenase2 oxidoreductase from ralstonia solanacearum
64 | d1ygya1 |
| not modelled | 68.2 | 28 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
65 | c2omeA_ |
| not modelled | 68.1 | 25 | PDB header:oxidoreductase Chain: A: PDB Molecule:c-terminal-binding protein 2; PDBTitle: crystal structure of human ctbp2 dehydrogenase complexed with nad(h)
66 | c3ijpA_ |
| not modelled | 67.4 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:dihydrodipicolinate reductase; PDBTitle: crystal structure of dihydrodipicolinate reductase from2 bartonella henselae at 2.0a resolution
67 | d1qp8a1 |
| not modelled | 65.8 | 24 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
68 | c1k3rA_ |
| not modelled | 65.4 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein mt0001; PDBTitle: crystal structure of the methyltransferase with a knot from2 methanobacterium thermoautotrophicum
69 | c2nacA_ |
| not modelled | 65.1 | 23 | PDB header:oxidoreductase(aldehyde(d),nad+(a)) Chain: A: PDB Molecule:nad-dependent formate dehydrogenase; PDBTitle: high resolution structures of holo and apo formate dehydrogenase
70 | c2j6iC_ |
| not modelled | 64.4 | 21 | PDB header:oxidoreductase Chain: C: PDB Molecule:formate dehydrogenase; PDBTitle: candida boidinii formate dehydrogenase (fdh) c-terminal2 mutant
71 | c1d4fD_ |
| not modelled | 63.0 | 25 | PDB header:hydrolase Chain: D: PDB Molecule:s-adenosylhomocysteine hydrolase; PDBTitle: crystal structure of recombinant rat-liver d244e mutant s-2 adenosylhomocysteine hydrolase
72 | d1mx3a1 |
| not modelled | 62.3 | 27 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
73 | c1gdhA_ |
| not modelled | 60.7 | 17 | PDB header:oxidoreductase(choh (d)-nad(p)+ (a)) Chain: A: PDB Molecule:d-glycerate dehydrogenase; PDBTitle: crystal structure of a nad-dependent d-glycerate2 dehydrogenase at 2.4 angstroms resolution
74 | c2g76A_ |
| not modelled | 60.1 | 24 | PDB header:oxidoreductase Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase; PDBTitle: crystal structure of human 3-phosphoglycerate dehydrogenase
75 | c3evtA_ |
| not modelled | 59.6 | 26 | PDB header:oxidoreductase Chain: A: PDB Molecule:phosphoglycerate dehydrogenase; PDBTitle: crystal structure of phosphoglycerate dehydrogenase from2 lactobacillus plantarum
76 | d1k3ra2 |
| not modelled | 58.3 | 16 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:Hypothetical protein MTH1 (MT0001), dimerisation domain
77 | c3gvpB_ |
| not modelled | 57.9 | 20 | PDB header:hydrolase Chain: B: PDB Molecule:adenosylhomocysteinase 3; PDBTitle: human sahh-like domain of human adenosylhomocysteinase 3
78 | c3dhyC_ |
| not modelled | 57.3 | 29 | PDB header:hydrolase Chain: C: PDB Molecule:adenosylhomocysteinase; PDBTitle: crystal structures of mycobacterium tuberculosis s-adenosyl-l-2 homocysteine hydrolase in ternary complex with substrate and3 inhibitors
79 | d1gdha1 |
| not modelled | 56.2 | 17 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
80 | c1j4aA_ |
| not modelled | 54.3 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:d-lactate dehydrogenase; PDBTitle: insights into domain closure, substrate specificity and2 catalysis of d-lactate dehydrogenase from lactobacillus3 bulgaricus
81 | d1sc6a1 |
| not modelled | 54.2 | 25 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
82 | c1qp8A_ |
| not modelled | 52.4 | 22 | PDB header:oxidoreductase Chain: A: PDB Molecule:formate dehydrogenase; PDBTitle: crystal structure of a putative formate dehydrogenase from2 pyrobaculum aerophilum
83 | c2w2kB_ |
| not modelled | 51.3 | 29 | PDB header:oxidoreductase Chain: B: PDB Molecule:d-mandelate dehydrogenase; PDBTitle: crystal structure of the apo forms of rhodotorula graminis2 d-mandelate dehydrogenase at 1.8a.
84 | d1vh0a_ |
| not modelled | 51.1 | 22 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
85 | c1mldA_ |
| not modelled | 50.3 | 22 | PDB header:oxidoreductase(nad(a)-choh(d)) Chain: A: PDB Molecule:malate dehydrogenase; PDBTitle: refined structure of mitochondrial malate dehydrogenase2 from porcine heart and the consensus structure for3 dicarboxylic acid oxidoreductases
86 | c3oneA_ |
| not modelled | 49.9 | 22 | PDB header:hydrolase/hydrolase substrate Chain: A: PDB Molecule:adenosylhomocysteinase; PDBTitle: crystal structure of lupinus luteus s-adenosyl-l-homocysteine2 hydrolase in complex with adenine
87 | d1o6da_ |
| not modelled | 49.2 | 19 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
88 | c2a9fB_ |
| not modelled | 48.4 | 20 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative malic enzyme ((s)-malate:nad+ PDBTitle: crystal structure of a putative malic enzyme ((s)-2 malate:nad+ oxidoreductase (decarboxylating))
89 | d2atca2 |
| not modelled | 48.0 | 13 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
90 | c3tpfF_ |
| not modelled | 47.9 | 14 | PDB header:transferase Chain: F: PDB Molecule:ornithine carbamoyltransferase; PDBTitle: crystal structure of anabolic ornithine carbamoyltransferase from2 campylobacter jejuni subsp. jejuni nctc 11168
91 | c2at2B_ |
| not modelled | 47.6 | 15 | PDB header: PDB COMPND:
92 | d1oi7a1 |
| not modelled | 47.5 | 23 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:CoA-binding domain
93 | c3hg7A_ |
| not modelled | 47.1 | 22 | PDB header:oxidoreductase Chain: A: PDB Molecule:d-isomer specific 2-hydroxyacid dehydrogenase family PDBTitle: crystal structure of d-isomer specific 2-hydroxyacid dehydrogenase2 family protein from aeromonas salmonicida subsp. salmonicida a449
94 | c2gcgB_ |
| not modelled | 47.0 | 22 | PDB header:oxidoreductase Chain: B: PDB Molecule:glyoxylate reductase/hydroxypyruvate reductase; PDBTitle: ternary crystal structure of human glyoxylate2 reductase/hydroxypyruvate reductase
95 | c3pqeD_ |
| not modelled | 46.9 | 17 | PDB header:oxidoreductase Chain: D: PDB Molecule:l-lactate dehydrogenase; PDBTitle: crystal structure of l-lactate dehydrogenase from bacillus subtilis2 with h171c mutation
96 | d1diha1 |
| not modelled | 46.8 | 18 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
97 | c2pi1C_ |
| not modelled | 45.8 | 22 | PDB header:oxidoreductase Chain: C: PDB Molecule:d-lactate dehydrogenase; PDBTitle: crystal structure of d-lactate dehydrogenase from aquifex2 aeolicus complexed with nad and lactic acid
98 | d1ns5a_ |
| not modelled | 45.7 | 21 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
99 | c2dbqA_ |
| not modelled | 45.2 | 20 | PDB header:oxidoreductase Chain: A: PDB Molecule:glyoxylate reductase; PDBTitle: crystal structure of glyoxylate reductase (ph0597) from pyrococcus2 horikoshii ot3, complexed with nadp (i41)
100 | c3bazA_ |
| not modelled | 44.9 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:hydroxyphenylpyruvate reductase; PDBTitle: structure of hydroxyphenylpyruvate reductase from coleus blumei in2 complex with nadp+
101 | c1wwkA_ |
| not modelled | 43.3 | 24 | PDB header:oxidoreductase Chain: A: PDB Molecule:phosphoglycerate dehydrogenase; PDBTitle: crystal structure of phosphoglycerate dehydrogenase from pyrococcus2 horikoshii ot3
102 | c3ktdC_ |
| not modelled | 42.9 | 23 | PDB header:oxidoreductase Chain: C: PDB Molecule:prephenate dehydrogenase; PDBTitle: crystal structure of a putative prephenate dehydrogenase (cgl0226)2 from corynebacterium glutamicum atcc 13032 at 2.60 a resolution
103 | c1drwA_ |
| not modelled | 42.3 | 17 | PDB header:oxidoreductase Chain: A: PDB Molecule:dihydrodipicolinate reductase; PDBTitle: escherichia coli dhpr/nhdh complex
104 | c1gpjA_ |
| not modelled | 42.3 | 21 | PDB header:reductase Chain: A: PDB Molecule:glutamyl-trna reductase; PDBTitle: glutamyl-trna reductase from methanopyrus kandleri
105 | c3n58D_ |
| not modelled | 42.0 | 27 | PDB header:hydrolase Chain: D: PDB Molecule:adenosylhomocysteinase; PDBTitle: crystal structure of s-adenosyl-l-homocysteine hydrolase from brucella2 melitensis in ternary complex with nad and adenosine, orthorhombic3 form
106 | c3d0oA_ |
| not modelled | 42.0 | 15 | PDB header:oxidoreductase Chain: A: PDB Molecule:l-lactate dehydrogenase 1; PDBTitle: crystal structure of lactate dehydrogenase from2 staphylococcus aureus
107 | c1z85B_ |
| not modelled | 40.8 | 11 | PDB header:transferase Chain: B: PDB Molecule:hypothetical protein tm1380; PDBTitle: crystal structure of a predicted rna methyltransferase (tm1380) from2 thermotoga maritima msb8 at 2.12 a resolution
108 | d1to0a_ |
| not modelled | 40.7 | 13 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
109 | c1v8bA_ |
| not modelled | 40.2 | 25 | PDB header:hydrolase Chain: A: PDB Molecule:adenosylhomocysteinase; PDBTitle: crystal structure of a hydrolase
110 | c1ybaC_ |
| not modelled | 39.9 | 25 | PDB header:oxidoreductase Chain: C: PDB Molecule:d-3-phosphoglycerate dehydrogenase; PDBTitle: the active form of phosphoglycerate dehydrogenase
111 | c1dxyA_ |
| not modelled | 39.1 | 13 | PDB header:oxidoreductase Chain: A: PDB Molecule:d-2-hydroxyisocaproate dehydrogenase; PDBTitle: structure of d-2-hydroxyisocaproate dehydrogenase
112 | d7reqb2 |
| not modelled | 37.6 | 23 | Fold:Flavodoxin-like Superfamily:Cobalamin (vitamin B12)-binding domain Family:Cobalamin (vitamin B12)-binding domain
113 | d1gpja2 |
| not modelled | 37.1 | 26 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain
114 | c2d4aC_ |
| not modelled | 36.1 | 23 | PDB header:oxidoreductase Chain: C: PDB Molecule:malate dehydrogenase; PDBTitle: structure of the malate dehydrogenase from aeropyrum pernix
115 | c2d0iC_ |
| not modelled | 35.7 | 24 | PDB header:oxidoreductase Chain: C: PDB Molecule:dehydrogenase; PDBTitle: crystal structure ph0520 protein from pyrococcus horikoshii ot3
116 | c2eklA_ |
| not modelled | 35.0 | 20 | PDB header:oxidoreductase Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase; PDBTitle: structure of st1218 protein from sulfolobus tokodaii
117 | c3oirA_ |
| not modelled | 34.5 | 24 | PDB header:transport protein Chain: A: PDB Molecule:sulfate transporter sulfate transporter family protein; PDBTitle: crystal structure of sulfate transporter family protein from wolinella2 succinogenes
118 | c2fnzA_ |
| not modelled | 32.7 | 16 | PDB header:oxidoreductase Chain: A: PDB Molecule:lactate dehydrogenase; PDBTitle: crystal structure of the lactate dehydrogenase from cryptosporidium2 parvum complexed with cofactor (b-nicotinamide adenine dinucleotide)3 and inhibitor (oxamic acid)
119 | c2cukC_ |
| not modelled | 32.6 | 27 | PDB header:oxidoreductase Chain: C: PDB Molecule:glycerate dehydrogenase/glyoxylate reductase; PDBTitle: crystal structure of tt0316 protein from thermus thermophilus hb8
120 | c1xdwA_ |
| not modelled | 32.2 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:nad+-dependent (r)-2-hydroxyglutarate PDBTitle: nad+-dependent (r)-2-hydroxyglutarate dehydrogenase from2 acidaminococcus fermentans

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