Phyre 2 Results for P0AGJ2

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Email | l.a.kelley@imperial.ac.uk
Description | P0AGJ2
Date | Thu Jan 5 11:29:18 GMT 2012
Unique Job ID | 03822049b05be78c

Summary |

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

Model (left) based on template c1zjrA_
Top template information
PDB header:transferase Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase; PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme
Confidence and coverage
Confidence: | 100.0% | Coverage: | 85%
195 residues ( 85% 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 | N | P | T | R | Y | A | R | I | C | E | M | L | A | R | R | Q | P | D | L | T | V | C | M | E | Q | V | H | K | P | H | N | V | S | A | I | I | R | T | A | D | A | V | G | V | H | E | V | H | A | V | W | P | G | S | R | M | R | T | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | A | S | A | A | A | G | S | N | S | W | V | Q | V | K | T | H | R | T | I | G | D | A | V | A | H | L | K | G | Q | G | M | Q | I | L | A | T | H | L | S | D | N | A | V | D | F | R | E | I | D | Y | T | R | P | T | C | I | L | M | G | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | E | K | T | G | I | T | Q | E | A | L | A | L | A | D | Q | D | I | I | I | P | M | I | G | M | V | Q | S | L | N | V | S | V | A | S | A | L | I | L | Y | E | A | Q | R | Q | R | Q | N | A | G | M | Y | L | R | E | N | S | M | L | P | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | .
Sequence |  | A | E | Q | Q | R | L | L | F | E | G | G | Y | P | V | L | A | K | V | A | K | R | K | G | L | P | Y | P | H | V | N | Q | Q | G | E | I | E | A | D | A | D | W | W | A | T | M | Q | A | A | G
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 |
| c1zjrA_ |

### PDB 1zjr chain A

Region: 1 - 197
Aligned: 195
Modelled: 195
Confidence: 100.0%
Identity: 42%
PDB header:transferase
Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase;
PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme

Phyre2
2 |
| d1v2xa_ |

### PDB 1v2x chain A

Region: 2 - 190
Aligned: 187
Modelled: 187
Confidence: 100.0%
Identity: 53%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
3 |
| d1gz0a1 |

### PDB 1gz0 chain A domain 1

Region: 7 - 165
Aligned: 158
Modelled: 159
Confidence: 100.0%
Identity: 28%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
4 |
| c1gz0G_ |

### PDB 1gz0 chain G

Region: 7 - 165
Aligned: 158
Modelled: 151
Confidence: 100.0%
Identity: 28%
PDB header:transferase
Chain: G: PDB Molecule:hypothetical trna/rrna methyltransferase yjfh;
PDBTitle: 23s ribosomal rna g2251 2'o-methyltransferase rlmb

Phyre2
5 |
| c2ha8A_ |

### PDB 2ha8 chain A

Region: 13 - 168
Aligned: 156
Modelled: 156
Confidence: 100.0%
Identity: 22%
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
6 |
| c1x7pB_ |

### PDB 1x7p chain B

Region: 13 - 166
Aligned: 153
Modelled: 153
Confidence: 100.0%
Identity: 29%
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
7 |
| c1ipaA_ |

### PDB 1ipa chain A

Region: 13 - 166
Aligned: 152
Modelled: 152
Confidence: 100.0%
Identity: 28%
PDB header:transferase
Chain: A: PDB Molecule:rna 2'-o-ribose methyltransferase;
PDBTitle: crystal structure of rna 2'-o ribose methyltransferase

Phyre2
8 |
| c2i6dA_ |

### PDB 2i6d chain A

Region: 14 - 164
Aligned: 151
Modelled: 150
Confidence: 100.0%
Identity: 28%
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
9 |
| c3gyqB_ |

### PDB 3gyq chain B

Region: 16 - 169
Aligned: 153
Modelled: 153
Confidence: 100.0%
Identity: 24%
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
10 |
| d1ipaa1 |

### PDB 1ipa chain A domain 1

Region: 13 - 167
Aligned: 153
Modelled: 153
Confidence: 100.0%
Identity: 27%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
11 |
| c3ic6A_ |

### PDB 3ic6 chain A

Region: 13 - 197
Aligned: 178
Modelled: 175
Confidence: 100.0%
Identity: 16%
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
12 |
| d1mxia_ |

### PDB 1mxi chain A

Region: 20 - 171
Aligned: 149
Modelled: 149
Confidence: 100.0%
Identity: 23%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2
13 |
| c3ilkB_ |

### PDB 3ilk chain B

Region: 18 - 208
Aligned: 182
Modelled: 186
Confidence: 100.0%
Identity: 18%
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
14 |
| c3onpA_ |

### PDB 3onp chain A

Region: 19 - 164
Aligned: 146
Modelled: 146
Confidence: 100.0%
Identity: 23%
PDB header:transferase
Chain: A: PDB Molecule:trna/rrna methyltransferase (spou);
PDBTitle: crystal structure of trna/rrna methyltransferase spou from rhodobacter2 sphaeroides

Phyre2
15 |
| c3e5yB_ |

### PDB 3e5y chain B

Region: 20 - 169
Aligned: 136
Modelled: 136
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
16 |
| c3l8uA_ |

### PDB 3l8u chain A

Region: 21 - 175
Aligned: 148
Modelled: 148
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
17 |
| c3ktyA_ |

### PDB 3kty chain A

Region: 18 - 165
Aligned: 147
Modelled: 148
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: A: PDB Molecule:probable methyltransferase;
PDBTitle: crystal structure of probable methyltransferase from bordetella2 pertussis tohama i

Phyre2
18 |
| c3dcmX_ |

### PDB 3dcm chain X

Region: 12 - 162
Aligned: 147
Modelled: 147
Confidence: 99.9%
Identity: 18%
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
19 |
| d1vhka2 |

### PDB 1vhk chain A domain 2

Region: 14 - 165
Aligned: 150
Modelled: 150
Confidence: 97.4%
Identity: 15%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: YggJ C-terminal domain-like

Phyre2
20 |
| c1vhkA_ |

### PDB 1vhk chain A

Region: 14 - 161
Aligned: 146
Modelled: 146
Confidence: 97.0%
Identity: 15%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yqeu;
PDBTitle: crystal structure of an hypothetical protein

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1zjrA_ |
|  | 100.0 | 42 | PDB header:transferase Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase; PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme
2 | d1v2xa_ |
|  | 100.0 | 53 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
3 | d1gz0a1 |
|  | 100.0 | 28 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
4 | c1gz0G_ |
|  | 100.0 | 28 | PDB header:transferase Chain: G: PDB Molecule:hypothetical trna/rrna methyltransferase yjfh; PDBTitle: 23s ribosomal rna g2251 2'o-methyltransferase rlmb
5 | c2ha8A_ |
|  | 100.0 | 22 | 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
6 | c1x7pB_ |
|  | 100.0 | 29 | 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
7 | c1ipaA_ |
|  | 100.0 | 28 | PDB header:transferase Chain: A: PDB Molecule:rna 2'-o-ribose methyltransferase; PDBTitle: crystal structure of rna 2'-o ribose methyltransferase
8 | c2i6dA_ |
|  | 100.0 | 28 | 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.
9 | c3gyqB_ |
|  | 100.0 | 24 | PDB header:transferase Chain: B: PDB Molecule:rrna (adenosine-2'-o-)-methyltransferase; PDBTitle: structure of the thiostrepton-resistance methyltransferase2 s-adenosyl-l-methionine complex
10 | d1ipaa1 |
|  | 100.0 | 27 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
11 | c3ic6A_ |
|  | 100.0 | 16 | 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
12 | d1mxia_ |
|  | 100.0 | 23 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:SpoU-like RNA 2'-O ribose methyltransferase
13 | c3ilkB_ |
|  | 100.0 | 18 | 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
14 | c3onpA_ |
|  | 100.0 | 23 | PDB header:transferase Chain: A: PDB Molecule:trna/rrna methyltransferase (spou); PDBTitle: crystal structure of trna/rrna methyltransferase spou from rhodobacter2 sphaeroides
15 | 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
16 | 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
17 | c3ktyA_ |
|  | 100.0 | 21 | PDB header:transferase Chain: A: PDB Molecule:probable methyltransferase; PDBTitle: crystal structure of probable methyltransferase from bordetella2 pertussis tohama i
18 | c3dcmX_ |
|  | 99.9 | 18 | 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
19 | d1vhka2 |
|  | 97.4 | 15 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YggJ C-terminal domain-like
20 | c1vhkA_ |
|  | 97.0 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein yqeu; PDBTitle: crystal structure of an hypothetical protein
21 | c2yy8B_ |
| not modelled | 96.6 | 18 | 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
22 | c3kw2A_ |
| not modelled | 96.4 | 13 | PDB header:transferase Chain: A: PDB Molecule:probable r-rna methyltransferase; PDBTitle: crystal structure of probable rrna-methyltransferase from2 porphyromonas gingivalis
23 | c2egwB_ |
| not modelled | 96.3 | 10 | PDB header:rna methyltransferase Chain: B: PDB Molecule:upf0088 protein aq_165; PDBTitle: crystal structure of rrna methyltransferase with sah ligand
24 | c3ai9X_ |
| not modelled | 96.2 | 16 | PDB header:transferase Chain: X: PDB Molecule:upf0217 protein mj1640; PDBTitle: crystal structure of duf358 protein reveals a putative spout-class2 rrna methyltransferase
25 | d1nxza2 |
| not modelled | 96.2 | 10 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YggJ C-terminal domain-like
26 | d2o3aa1 |
| not modelled | 95.4 | 18 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:AF0751-like
27 | c1vhyB_ |
| not modelled | 94.7 | 14 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein hi0303; PDBTitle: crystal structure of haemophilus influenzae protein hi0303, pfam2 duf558
28 | d2qwva1 |
| not modelled | 94.3 | 15 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:AF1056-like
29 | d1v6za2 |
| not modelled | 92.3 | 21 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YggJ C-terminal domain-like
30 | d2qmma1 |
| not modelled | 88.1 | 14 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:AF1056-like
31 | c2cx8B_ |
| not modelled | 86.9 | 19 | PDB header:transferase Chain: B: PDB Molecule:methyl transferase; PDBTitle: crystal structure of methyltransferase with ligand(sah)
32 | c1z85B_ |
| not modelled | 60.9 | 12 | 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
33 | c1k3rA_ |
| not modelled | 49.6 | 25 | 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
34 | d1ml4a2 |
| not modelled | 47.2 | 13 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
35 | d1a9xa3 |
| not modelled | 40.3 | 12 | Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:BC N-terminal domain-like
36 | c2v3jA_ |
| not modelled | 39.2 | 16 | PDB header:ribosomal protein Chain: A: PDB Molecule:essential for mitotic growth 1; PDBTitle: the yeast ribosome synthesis factor emg1 alpha beta knot2 fold methyltransferase
37 | d2b7oa1 |
| not modelled | 38.7 | 17 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class-II DAHP synthetase
38 | d1o6da_ |
| not modelled | 38.6 | 26 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
39 | d1j6ua2 |
| not modelled | 31.8 | 11 | Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain
40 | d1to0a_ |
| not modelled | 31.0 | 14 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
41 | d1k3ra2 |
| not modelled | 30.7 | 26 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:Hypothetical protein MTH1 (MT0001), dimerisation domain
42 | c1j6uA_ |
| not modelled | 30.0 | 13 | PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate-alanine ligase murc; PDBTitle: crystal structure of udp-n-acetylmuramate-alanine ligase2 murc (tm0231) from thermotoga maritima at 2.3 a resolution
43 | d1vh0a_ |
| not modelled | 29.8 | 11 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
44 | d1ns5a_ |
| not modelled | 29.6 | 26 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
45 | d1mx3a1 |
| not modelled | 29.3 | 16 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
46 | d1ekxa2 |
| not modelled | 28.9 | 15 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
47 | c2omeA_ |
| not modelled | 27.0 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:c-terminal-binding protein 2; PDBTitle: crystal structure of human ctbp2 dehydrogenase complexed with nad(h)
48 | d1qpoa1 |
| not modelled | 25.7 | 9 | Fold:TIM beta/alpha-barrel Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like Family:NadC C-terminal domain-like
49 | c2wl8D_ |
| not modelled | 25.7 | 14 | PDB header:protein transport Chain: D: PDB Molecule:peroxisomal biogenesis factor 19; PDBTitle: x-ray crystal structure of pex19p
50 | d1o4ua1 |
| not modelled | 25.1 | 16 | Fold:TIM beta/alpha-barrel Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like Family:NadC C-terminal domain-like
51 | c3gg9C_ |
| not modelled | 24.8 | 6 | 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
52 | c3o7bA_ |
| not modelled | 23.2 | 16 | PDB header:transferase Chain: A: PDB Molecule:ribosome biogenesis nep1 rna methyltransferase; PDBTitle: crystal structure of archaeoglobus fulgidus nep1 bound to s-2 adenosylhomocysteine
53 | c3czpA_ |
| not modelled | 21.2 | 22 | PDB header:transferase Chain: A: PDB Molecule:putative polyphosphate kinase 2; PDBTitle: crystal structure of putative polyphosphate kinase 2 from pseudomonas2 aeruginosa pa01
54 | c1qpoA_ |
| not modelled | 20.4 | 9 | PDB header:transferase Chain: A: PDB Molecule:quinolinate acid phosphoribosyl transferase; PDBTitle: quinolinate phosphoribosyl transferase (qaprtase) apo-enzyme from2 mycobacterium tuberculosis
55 | c2y0fD_ |
| not modelled | 19.9 | 29 | PDB header:oxidoreductase Chain: D: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; PDBTitle: structure of gcpe (ispg) from thermus thermophilus hb27
56 | c2o8vA_ |
| not modelled | 19.8 | 15 | PDB header:oxidoreductase Chain: A: PDB Molecule:phosphoadenosine phosphosulfate reductase; PDBTitle: paps reductase in a covalent complex with thioredoxin c35a
57 | c2oq2B_ |
| not modelled | 19.0 | 15 | PDB header:oxidoreductase Chain: B: PDB Molecule:phosphoadenosine phosphosulfate reductase; PDBTitle: crystal structure of yeast paps reductase with pap, a product complex
58 | d1sura_ |
| not modelled | 18.1 | 15 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Adenine nucleotide alpha hydrolases-like Family:PAPS reductase-like
59 | c2x3yA_ |
| not modelled | 18.0 | 19 | PDB header:isomerase Chain: A: PDB Molecule:phosphoheptose isomerase; PDBTitle: crystal structure of gmha from burkholderia pseudomallei
60 | c2yqeA_ |
| not modelled | 17.7 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:jumonji/arid domain-containing protein 1d; PDBTitle: solution structure of the arid domain of jarid1d protein
61 | d1nkua_ |
| not modelled | 17.3 | 29 | Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag)
62 | c2jg6A_ |
| not modelled | 16.8 | 25 | PDB header:hydrolase Chain: A: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of a 3-methyladenine dna glycosylase i2 from staphylococcus aureus
63 | c3ajfA_ |
| not modelled | 16.6 | 25 | PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: structural insigths into dsrna binding and rna silencing suppression2 by ns3 protein of rice hoja blanca tenuivirus
64 | c2zy3A_ |
| not modelled | 16.4 | 26 | PDB header:lyase Chain: A: PDB Molecule:l-aspartate beta-decarboxylase; PDBTitle: dodecameric l-aspartate beta-decarboxylase
65 | c2w2kB_ |
| not modelled | 16.3 | 10 | 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.
66 | c3q4gA_ |
| not modelled | 16.2 | 17 | PDB header:ligase Chain: A: PDB Molecule:nh(3)-dependent nad(+) synthetase; PDBTitle: structure of nad synthetase from vibrio cholerae
67 | c1dvpA_ |
| not modelled | 15.3 | 16 | PDB header:transferase Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine PDBTitle: crystal structure of the vhs and fyve tandem domains of hrs,2 a protein involved in membrane trafficking and signal3 transduction
68 | c2fe3B_ |
| not modelled | 15.1 | 19 | PDB header:dna binding protein Chain: B: PDB Molecule:peroxide operon regulator; PDBTitle: the crystal structure of bacillus subtilis perr-zn reveals a novel2 zn(cys)4 structural redox switch
69 | c2b7pA_ |
| not modelled | 14.9 | 11 | PDB header:transferase Chain: A: PDB Molecule:probable nicotinate-nucleotide pyrophosphorylase; PDBTitle: crystal structure of quinolinic acid phosphoribosyltransferase from2 helicobacter pylori
70 | d2f06a1 |
| not modelled | 14.8 | 17 | Fold:Ferredoxin-like Superfamily:ACT-like Family:BT0572-like
71 | d2v3ka1 |
| not modelled | 14.5 | 17 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:EMG1/NEP1-like
72 | c2jbmA_ |
| not modelled | 14.5 | 13 | PDB header:transferase Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase; PDBTitle: qprtase structure from human
73 | c3mwmA_ |
| not modelled | 14.4 | 13 | PDB header:transcription Chain: A: PDB Molecule:putative metal uptake regulation protein; PDBTitle: graded expression of zinc-responsive genes through two regulatory2 zinc-binding sites in zur
74 | d1e8ca2 |
| not modelled | 14.4 | 8 | Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain
75 | d1x7da_ |
| not modelled | 13.4 | 15 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Ornithine cyclodeaminase-like
76 | c2qipA_ |
| not modelled | 13.4 | 18 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein of unknown function vpa0982; PDBTitle: crystal structure of a protein of unknown function vpa0982 from vibrio2 parahaemolyticus rimd 2210633
77 | d1o17a2 |
| not modelled | 12.8 | 45 | Fold:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Family:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
78 | c2o03A_ |
| not modelled | 12.6 | 15 | PDB header:gene regulation Chain: A: PDB Molecule:probable zinc uptake regulation protein furb; PDBTitle: crystal structure of furb from m. tuberculosis- a zinc uptake2 regulator
79 | c3fxaA_ |
| not modelled | 12.5 | 12 | PDB header:sugar binding protein Chain: A: PDB Molecule:sis domain protein; PDBTitle: crystal structure of a putative sugar-phosphate isomerase2 (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 a3 resolution
80 | c2goyC_ |
| not modelled | 12.4 | 19 | PDB header:oxidoreductase Chain: C: PDB Molecule:adenosine phosphosulfate reductase; PDBTitle: crystal structure of assimilatory adenosine 5'-2 phosphosulfate reductase with bound aps
81 | d2gy9b1 |
| not modelled | 12.3 | 23 | Fold:Flavodoxin-like Superfamily:Ribosomal protein S2 Family:Ribosomal protein S2
82 | d1dvpa1 |
| not modelled | 12.1 | 19 | Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:VHS domain
83 | c2nacA_ |
| not modelled | 11.8 | 12 | 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
84 | d1pg5a2 |
| not modelled | 11.3 | 13 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
85 | c2zkqb_ |
| not modelled | 11.2 | 18 | PDB header:ribosomal protein/rna Chain: B: PDB Molecule:rna expansion segment es3; PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
86 | c3navB_ |
| not modelled | 10.8 | 7 | PDB header:lyase Chain: B: PDB Molecule:tryptophan synthase alpha chain; PDBTitle: crystal structure of an alpha subunit of tryptophan synthase from2 vibrio cholerae o1 biovar el tor str. n16961
87 | d1q9ua_ |
| not modelled | 10.4 | 21 | Fold:TBP-like Superfamily:TT1751-like Family:TT1751-like
88 | c1x3lA_ |
| not modelled | 10.3 | 22 | PDB header:transferase Chain: A: PDB Molecule:hypothetical protein ph0495; PDBTitle: crystal structure of the ph0495 protein from pyrococccus horikoshii2 ot3
89 | d1oaoc_ |
| not modelled | 10.0 | 15 | Fold:Prismane protein-like Superfamily:Prismane protein-like Family:Acetyl-CoA synthase
90 | c1o4uA_ |
| not modelled | 9.2 | 16 | PDB header:transferase Chain: A: PDB Molecule:type ii quinolic acid phosphoribosyltransferase; PDBTitle: crystal structure of a nicotinate nucleotide pyrophosphorylase2 (tm1645) from thermotoga maritima at 2.50 a resolution
91 | d1kkxa_ |
| not modelled | 9.2 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:ARID-like Family:ARID domain
92 | c3hpbA_ |
| not modelled | 9.2 | 23 | PDB header:protein transport Chain: A: PDB Molecule:snx5 protein; PDBTitle: crystal structure of snx5-px domain in p212121 space group
93 | c3bchA_ |
| not modelled | 9.1 | 21 | PDB header:cell adhesion, ribosomal protein Chain: A: PDB Molecule:40s ribosomal protein sa; PDBTitle: crystal structure of the human laminin receptor precursor
94 | d1duvg2 |
| not modelled | 9.1 | 10 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
95 | d1hjra_ |
| not modelled | 8.9 | 33 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:RuvC resolvase
96 | d1dxya1 |
| not modelled | 8.9 | 11 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain
97 | c2kwuA_ |
| not modelled | 8.7 | 40 | PDB header:protein binding/signaling protein Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution structure of ubm2 of murine polymerase iota in complex with2 ubiquitin
98 | c3l0gD_ |
| not modelled | 8.7 | 11 | PDB header:transferase Chain: D: PDB Molecule:nicotinate-nucleotide pyrophosphorylase; PDBTitle: crystal structure of nicotinate-nucleotide pyrophosphorylase from2 ehrlichia chaffeensis at 2.05a resolution
99 | c3bbnB_ |
| not modelled | 8.7 | 13 | PDB header:ribosome Chain: B: PDB Molecule:ribosomal protein s2; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome.

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