Phyre 2 Results for P60340

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Email | l.a.kelley@imperial.ac.uk
Description | P60340
Date | Thu Jan 5 12:06:43 GMT 2012
Unique Job ID | 1178dd69661e9c4d

Summary |

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

Model (left) based on template c1k8wA_
Top template information
PDB header:lyase/rna Chain: A: PDB Molecule:trna pseudouridine synthase b; PDBTitle: crystal structure of the e. coli pseudouridine synthase2 trub bound to a t stem-loop rna
Confidence and coverage
Confidence: | 100.0% | Coverage: | 96%
303 residues ( 96% 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 | S | R | P | R | R | R | G | R | D | I | N | G | V | L | L | L | D | K | P | Q | G | M | S | S | N | D | A | L | Q | K | V | K | R | I | Y | N | A | N | R | A | G | H | T | G | A | L | D | P | L | A | T | G | M | L | P | I | C | L | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | A | T | K | F | S | Q | Y | L | L | D | S | D | K | R | Y | R | V | I | A | R | L | G | Q | R | T | D | T | S | D | A | D | G | Q | I | V | E | E | R | P | V | T | F | S | A | E | Q | L | A | A | A | L | D | T | F | R | G | D | I | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | Q | I | P | S | M | Y | S | A | L | K | Y | Q | G | K | K | L | Y | E | Y | A | R | Q | G | I | E | V | P | R | E | A | R | P | I | T | V | Y | E | L | L | F | I | R | H | E | G | N | E | L | E | L | E | I | H | C | S | K | G | T | Y | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | R | T | I | I | D | D | L | G | E | K | L | G | C | G | A | H | V | I | Y | L | R | R | L | A | V | S | K | Y | P | V | E | R | M | V | T | L | E | H | L | R | E | L | V | E | Q | A | E | Q | Q | D | I | P | A | A | E | L | L | D | P | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | L | M | P | M | D | S | P | A | S | D | Y | P | V | V | N | L | P | L | T | S | S | V | Y | F | K | N | G | N | P | V | R | T | S | G | A | P | L | E | G | L | V | R | V | T | E | G | E | N | G | K | F | I | G | M | G | E | I | D | D | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | .
Sequence |  | G | R | V | A | P | R | R | L | V | V | E | Y | P | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |

Confidence Key
High(9) |  |  |  |  |  |  |  |  |  |  | Low (0)

? | Disordered
| Alpha helix
| Beta strand

Domain analysis |

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank | Aligned region
--- | ---
1 |
| c1k8wA_ |

### PDB 1k8w chain A

Region: 10 - 312
Aligned: 303
Modelled: 302
Confidence: 100.0%
Identity: 100%
PDB header:lyase/rna
Chain: A: PDB Molecule:trna pseudouridine synthase b;
PDBTitle: crystal structure of the e. coli pseudouridine synthase2 trub bound to a t stem-loop rna

Phyre2
2 |
| d1k8wa5 |

### PDB 1k8w chain A domain 5

Region: 10 - 250
Aligned: 241
Modelled: 241
Confidence: 100.0%
Identity: 100%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase II TruB

Phyre2
3 |
| d1r3ea2 |

### PDB 1r3e chain A domain 2

Region: 11 - 250
Aligned: 227
Modelled: 240
Confidence: 100.0%
Identity: 33%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase II TruB

Phyre2
4 |
| c1sgvA_ |

### PDB 1sgv chain A

Region: 13 - 313
Aligned: 257
Modelled: 267
Confidence: 100.0%
Identity: 32%
PDB header:lyase
Chain: A: PDB Molecule:trna pseudouridine synthase b;
PDBTitle: structure of trna psi55 pseudouridine synthase (trub)

Phyre2
5 |
| c2ey4A_ |

### PDB 2ey4 chain A

Region: 7 - 311
Aligned: 268
Modelled: 271
Confidence: 100.0%
Identity: 29%
PDB header:isomerase/biosynthetic protein
Chain: A: PDB Molecule:probable trna pseudouridine synthase b;
PDBTitle: crystal structure of a cbf5-nop10-gar1 complex

Phyre2
6 |
| c3uaiA_ |

### PDB 3uai chain A

Region: 12 - 313
Aligned: 263
Modelled: 265
Confidence: 100.0%
Identity: 28%
PDB header:isomerase/chaperone
Chain: A: PDB Molecule:h/aca ribonucleoprotein complex subunit 4;
PDBTitle: structure of the shq1-cbf5-nop10-gar1 complex from saccharomyces2 cerevisiae

Phyre2
7 |
| c2apoA_ |

### PDB 2apo chain A

Region: 8 - 313
Aligned: 259
Modelled: 261
Confidence: 100.0%
Identity: 31%
PDB header:isomerase/rna binding protein
Chain: A: PDB Molecule:probable trna pseudouridine synthase b;
PDBTitle: crystal structure of the methanococcus jannaschii cbf52 nop10 complex

Phyre2
8 |
| d2ey4a2 |

### PDB 2ey4 chain A domain 2

Region: 12 - 250
Aligned: 203
Modelled: 205
Confidence: 100.0%
Identity: 32%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase II TruB

Phyre2
9 |
| d1sgva2 |

### PDB 1sgv chain A domain 2

Region: 12 - 248
Aligned: 198
Modelled: 202
Confidence: 100.0%
Identity: 37%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase II TruB

Phyre2
10 |
| c1ze2B_ |

### PDB 1ze2 chain B

Region: 11 - 303
Aligned: 209
Modelled: 234
Confidence: 100.0%
Identity: 29%
PDB header:lyase/rna
Chain: B: PDB Molecule:trna pseudouridine synthase b;
PDBTitle: conformational change of pseudouridine 55 synthase upon its2 association with rna substrate

Phyre2
11 |
| d2apoa2 |

### PDB 2apo chain A domain 2

Region: 12 - 249
Aligned: 191
Modelled: 193
Confidence: 100.0%
Identity: 32%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase II TruB

Phyre2
12 |
| c2omlA_ |

### PDB 2oml chain A

Region: 14 - 212
Aligned: 157
Modelled: 163
Confidence: 99.2%
Identity: 20%
PDB header:isomerase
Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase e;
PDBTitle: crystal structure of e. coli pseudouridine synthase rlue

Phyre2
13 |
| d1k8wa3 |

### PDB 1k8w chain A domain 3

Region: 251 - 312
Aligned: 62
Modelled: 61
Confidence: 99.1%
Identity: 100%
Fold: PUA domain-like
Superfamily: PUA domain-like
Family: PUA domain

Phyre2
14 |
| c2olwB_ |

### PDB 2olw chain B

Region: 14 - 212
Aligned: 155
Modelled: 163
Confidence: 98.9%
Identity: 20%
PDB header:isomerase
Chain: B: PDB Molecule:ribosomal large subunit pseudouridine synthase e;
PDBTitle: crystal structure of e. coli pseudouridine synthase rlue

Phyre2
15 |
| c2v9kA_ |

### PDB 2v9k chain A

Region: 70 - 200
Aligned: 99
Modelled: 114
Confidence: 98.3%
Identity: 17%
PDB header:lyase
Chain: A: PDB Molecule:uncharacterized protein flj32312;
PDBTitle: crystal structure of human pus10, a novel pseudouridine2 synthase.

Phyre2
16 |
| d1vioa1 |

### PDB 1vio chain A domain 1

Region: 14 - 222
Aligned: 151
Modelled: 159
Confidence: 98.2%
Identity: 23%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase RsuA/RluD

Phyre2
17 |
| c2gmlA_ |

### PDB 2gml chain A

Region: 14 - 224
Aligned: 148
Modelled: 159
Confidence: 98.1%
Identity: 22%
PDB header:isomerase
Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase f;
PDBTitle: crystal structure of catalytic domain of e.coli rluf

Phyre2
18 |
| c3dh3C_ |

### PDB 3dh3 chain C

Region: 14 - 212
Aligned: 141
Modelled: 147
Confidence: 98.1%
Identity: 18%
PDB header:isomerase/rna
Chain: C: PDB Molecule:ribosomal large subunit pseudouridine synthase f;
PDBTitle: crystal structure of rluf in complex with a 22 nucleotide2 rna substrate

Phyre2
19 |
| d1kska4 |

### PDB 1ksk chain A domain 4

Region: 14 - 215
Aligned: 145
Modelled: 152
Confidence: 98.0%
Identity: 19%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase RsuA/RluD

Phyre2
20 |
| c1vioA_ |

### PDB 1vio chain A

Region: 14 - 215
Aligned: 144
Modelled: 152
Confidence: 97.7%
Identity: 24%
PDB header:lyase
Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a;
PDBTitle: crystal structure of pseudouridylate synthase

Phyre2
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99 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1k8wA_ |
|  | 100.0 | 100 | PDB header:lyase/rna Chain: A: PDB Molecule:trna pseudouridine synthase b; PDBTitle: crystal structure of the e. coli pseudouridine synthase2 trub bound to a t stem-loop rna
2 | d1k8wa5 |
|  | 100.0 | 100 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB
3 | d1r3ea2 |
|  | 100.0 | 33 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB
4 | c1sgvA_ |
|  | 100.0 | 32 | PDB header:lyase Chain: A: PDB Molecule:trna pseudouridine synthase b; PDBTitle: structure of trna psi55 pseudouridine synthase (trub)
5 | c2ey4A_ |
|  | 100.0 | 29 | PDB header:isomerase/biosynthetic protein Chain: A: PDB Molecule:probable trna pseudouridine synthase b; PDBTitle: crystal structure of a cbf5-nop10-gar1 complex
6 | c3uaiA_ |
|  | 100.0 | 28 | PDB header:isomerase/chaperone Chain: A: PDB Molecule:h/aca ribonucleoprotein complex subunit 4; PDBTitle: structure of the shq1-cbf5-nop10-gar1 complex from saccharomyces2 cerevisiae
7 | c2apoA_ |
|  | 100.0 | 31 | PDB header:isomerase/rna binding protein Chain: A: PDB Molecule:probable trna pseudouridine synthase b; PDBTitle: crystal structure of the methanococcus jannaschii cbf52 nop10 complex
8 | d2ey4a2 |
|  | 100.0 | 32 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB
9 | d1sgva2 |
|  | 100.0 | 37 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB
10 | c1ze2B_ |
|  | 100.0 | 29 | PDB header:lyase/rna Chain: B: PDB Molecule:trna pseudouridine synthase b; PDBTitle: conformational change of pseudouridine 55 synthase upon its2 association with rna substrate
11 | d2apoa2 |
|  | 100.0 | 32 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB
12 | c2omlA_ |
|  | 99.2 | 20 | PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue
13 | d1k8wa3 |
|  | 99.1 | 100 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
14 | c2olwB_ |
|  | 98.9 | 20 | PDB header:isomerase Chain: B: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue
15 | c2v9kA_ |
|  | 98.3 | 17 | PDB header:lyase Chain: A: PDB Molecule:uncharacterized protein flj32312; PDBTitle: crystal structure of human pus10, a novel pseudouridine2 synthase.
16 | d1vioa1 |
|  | 98.2 | 23 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD
17 | c2gmlA_ |
|  | 98.1 | 22 | PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of catalytic domain of e.coli rluf
18 | c3dh3C_ |
|  | 98.1 | 18 | PDB header:isomerase/rna Chain: C: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of rluf in complex with a 22 nucleotide2 rna substrate
19 | d1kska4 |
|  | 98.0 | 19 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD
20 | c1vioA_ |
|  | 97.7 | 24 | PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridylate synthase
21 | d1v9ka_ |
| not modelled | 97.5 | 20 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD
22 | c3zv0D_ |
| not modelled | 97.5 | 19 | PDB header:cell cycle Chain: D: PDB Molecule:h/aca ribonucleoprotein complex subunit 4; PDBTitle: structure of the shq1p-cbf5p complex
23 | c2i82D_ |
| not modelled | 97.4 | 17 | PDB header:lyase/rna Chain: D: PDB Molecule:ribosomal large subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridine synthase rlua: indirect2 sequence readout through protein-induced rna structure
24 | c1kskA_ |
| not modelled | 97.3 | 21 | PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: structure of rsua
25 | c1qyuA_ |
| not modelled | 97.3 | 24 | PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: structure of the catalytic domain of 23s rrna pseudouridine2 synthase rlud
26 | d1v9fa_ |
| not modelled | 97.3 | 23 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD
27 | c1v9fA_ |
| not modelled | 97.3 | 23 | PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: crystal structure of catalytic domain of pseudouridine2 synthase rlud from escherichia coli
28 | d2apoa1 |
| not modelled | 95.5 | 23 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
29 | d1r3ea1 |
| not modelled | 93.5 | 20 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
30 | d2ey4a1 |
| not modelled | 93.1 | 13 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
31 | d1sgva1 |
| not modelled | 90.2 | 18 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
32 | c1q7hA_ |
| not modelled | 75.1 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: structure of a conserved pua domain protein from thermoplasma2 acidophilum
33 | c3d79A_ |
| not modelled | 74.1 | 19 | PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein ph0734; PDBTitle: crystal structure of hypothetical protein ph0734.1 from2 hyperthermophilic archaea pyrococcus horikoshii ot3
34 | d1iq8a3 |
| not modelled | 73.3 | 16 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
35 | d2as0a1 |
| not modelled | 68.7 | 21 | Fold:PUA domain-like Superfamily:PUA domain-like Family:Hypothetical RNA methyltransferase domain (HRMD)
36 | c1sb7A_ |
| not modelled | 67.7 | 12 | PDB header:lyase Chain: A: PDB Molecule:trna pseudouridine synthase d; PDBTitle: crystal structure of the e.coli pseudouridine synthase trud
37 | d1szwa_ |
| not modelled | 67.5 | 10 | Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:tRNA pseudouridine synthase TruD
38 | d2b78a1 |
| not modelled | 59.6 | 12 | Fold:PUA domain-like Superfamily:PUA domain-like Family:Hypothetical RNA methyltransferase domain (HRMD)
39 | c2b78A_ |
| not modelled | 57.3 | 10 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein smu.776; PDBTitle: a putative sam-dependent methyltransferase from2 streptococcus mutans
40 | d1q7ha1 |
| not modelled | 54.4 | 20 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
41 | c3r90E_ |
| not modelled | 50.6 | 11 | PDB header:rna binding protein Chain: E: PDB Molecule:malignant t cell-amplified sequence 1; PDBTitle: crystal structure of malignant t cell-amplified sequence 1 protein
42 | c1zs7A_ |
| not modelled | 44.3 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ape0525; PDBTitle: the structure of gene product ape0525 from aeropyrum pernix
43 | c2gagC_ |
| not modelled | 37.2 | 15 | PDB header:oxidoreductase Chain: C: PDB Molecule:heterotetrameric sarcosine oxidase gamma-subunit; PDBTitle: heteroteterameric sarcosine: structure of a diflavin metaloenzyme at2 1.85 a resolution
44 | c2frxD_ |
| not modelled | 35.0 | 21 | PDB header:transferase Chain: D: PDB Molecule:hypothetical protein yebu; PDBTitle: crystal structure of yebu, a m5c rna methyltransferase from e.coli
45 | c3m4xA_ |
| not modelled | 34.6 | 18 | PDB header:transferase Chain: A: PDB Molecule:nol1/nop2/sun family protein; PDBTitle: structure of a ribosomal methyltransferase
46 | c2xzmW_ |
| not modelled | 34.4 | 23 | PDB header:ribosome Chain: W: PDB Molecule:40s ribosomal protein s4; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1
47 | c2hjgA_ |
| not modelled | 29.6 | 8 | PDB header:hydrolase Chain: A: PDB Molecule:gtp-binding protein enga; PDBTitle: the crystal structure of the b. subtilis yphc gtpase in2 complex with gdp
48 | d2a2pa1 |
| not modelled | 28.4 | 21 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Selenoprotein W-related
49 | d2jn9a1 |
| not modelled | 28.2 | 9 | Fold:Split barrel-like Superfamily:YkvR-like Family:YkvR-like
50 | d1o7qa_ |
| not modelled | 24.8 | 21 | Fold:Nucleotide-diphospho-sugar transferases Superfamily:Nucleotide-diphospho-sugar transferases Family:alpha-1,3-galactosyltransferase-like
51 | d2cx1a1 |
| not modelled | 22.1 | 20 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
52 | d1lzia_ |
| not modelled | 21.7 | 15 | Fold:Nucleotide-diphospho-sugar transferases Superfamily:Nucleotide-diphospho-sugar transferases Family:alpha-1,3-galactosyltransferase-like
53 | d2gx8a1 |
| not modelled | 21.5 | 17 | Fold:NIF3 (NGG1p interacting factor 3)-like Superfamily:NIF3 (NGG1p interacting factor 3)-like Family:NIF3 (NGG1p interacting factor 3)-like
54 | c1z2zB_ |
| not modelled | 18.9 | 16 | PDB header:lyase Chain: B: PDB Molecule:probable trna pseudouridine synthase d; PDBTitle: crystal structure of the putative trna pseudouridine2 synthase d (trud) from methanosarcina mazei, northeast3 structural genomics target mar1
55 | d1mkya3 |
| not modelled | 18.9 | 3 | Fold:Alpha-lytic protease prodomain-like Superfamily:Probable GTPase Der, C-terminal domain Family:Probable GTPase Der, C-terminal domain
56 | c2gx8B_ |
| not modelled | 18.3 | 17 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:nif3-related protein; PDBTitle: the crystal stucture of bacillus cereus protein related to nif3
57 | d1k7ia2 |
| not modelled | 16.6 | 33 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Serralysin-like metalloprotease, catalytic (N-terminal) domain
58 | c3czxA_ |
| not modelled | 15.3 | 50 | PDB header:hydrolase Chain: A: PDB Molecule:putative n-acetylmuramoyl-l-alanine amidase; PDBTitle: the crystal structure of the putative n-acetylmuramoyl-l-2 alanine amidase from neisseria meningitidis
59 | d1g9ka2 |
| not modelled | 14.5 | 39 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Serralysin-like metalloprotease, catalytic (N-terminal) domain
60 | c1mkyA_ |
| not modelled | 14.3 | 3 | PDB header:ligand binding protein Chain: A: PDB Molecule:probable gtp-binding protein enga; PDBTitle: structural analysis of the domain interactions in der, a2 switch protein containing two gtpase domains
61 | c3m6wA_ |
| not modelled | 13.7 | 22 | PDB header:transferase Chain: A: PDB Molecule:rrna methylase; PDBTitle: multi-site-specific 16s rrna methyltransferase rsmf from thermus2 thermophilus in space group p21212 in complex with s-adenosyl-l-3 methionine
62 | c3or5A_ |
| not modelled | 13.6 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:thiol:disulfide interchange protein, thioredoxin family PDBTitle: crystal structure of thiol:disulfide interchange protein, thioredoxin2 family protein from chlorobium tepidum tls
63 | c3eykA_ |
| not modelled | 13.2 | 15 | PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha1 chain; PDBTitle: structure of influenza haemagglutinin in complex with an2 inhibitor of membrane fusion
64 | c3cmiA_ |
| not modelled | 11.8 | 13 | PDB header:oxidoreductase Chain: A: PDB Molecule:peroxiredoxin hyr1; PDBTitle: crystal structure of glutathione-dependent phospholipid peroxidase2 hyr1 from the yeast saccharomyces cerevisiae
65 | c1iq8B_ |
| not modelled | 11.5 | 16 | PDB header:transferase Chain: B: PDB Molecule:archaeosine trna-guanine transglycosylase; PDBTitle: crystal structure of archaeosine trna-guanine2 transglycosylase from pyrococcus horikoshii
66 | c2nydB_ |
| not modelled | 11.5 | 13 | PDB header:unknown function Chain: B: PDB Molecule:upf0135 protein sa1388; PDBTitle: crystal structure of staphylococcus aureus hypothetical protein sa1388
67 | d1sata2 |
| not modelled | 11.3 | 33 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Serralysin-like metalloprotease, catalytic (N-terminal) domain
68 | d3saka_ |
| not modelled | 11.1 | 29 | Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain
69 | c2owlA_ |
| not modelled | 10.0 | 12 | PDB header:recombination Chain: A: PDB Molecule:recombination-associated protein rdgc; PDBTitle: crystal structure of e. coli rdgc
70 | c3ne8A_ |
| not modelled | 10.0 | 50 | PDB header:hydrolase Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase; PDBTitle: the crystal structure of a domain from n-acetylmuramoyl-l-alanine2 amidase of bartonella henselae str. houston-1
71 | d1muga_ |
| not modelled | 9.1 | 19 | Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Mug-like
72 | c3kbgA_ |
| not modelled | 9.0 | 15 | PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s4e; PDBTitle: crystal structure of the 30s ribosomal protein s4e from2 thermoplasma acidophilum. northeast structural genomics3 consortium target tar28.
73 | c2d07A_ |
| not modelled | 8.8 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:g/t mismatch-specific thymine dna glycosylase; PDBTitle: crystal structure of sumo-3-modified thymine-dna glycosylase
74 | d1jwqa_ |
| not modelled | 8.3 | 50 | Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:N-acetylmuramoyl-L-alanine amidase-like
75 | d2gy9i1 |
| not modelled | 8.3 | 18 | Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components
76 | c1yp3C_ |
| not modelled | 7.7 | 24 | PDB header:transferase Chain: C: PDB Molecule:glucose-1-phosphate adenylyltransferase small PDBTitle: crystal structure of potato tuber adp-glucose2 pyrophosphorylase in complex with atp
77 | c2xs4A_ |
| not modelled | 7.4 | 28 | PDB header:hydrolase Chain: A: PDB Molecule:karilysin protease; PDBTitle: structure of karilysin catalytic mmp domain in complex with2 magnesium
78 | d1xova2 |
| not modelled | 7.3 | 29 | Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:N-acetylmuramoyl-L-alanine amidase-like
79 | c1pk1B_ |
| not modelled | 7.3 | 12 | PDB header:transcription repression Chain: B: PDB Molecule:sex comb on midleg cg9495-pa; PDBTitle: hetero sam domain structure of ph and scm.
80 | d1hv5a_ |
| not modelled | 7.3 | 26 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Matrix metalloproteases, catalytic domain
81 | c1mszA_ |
| not modelled | 7.3 | 21 | PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein smubp-2; PDBTitle: solution structure of the r3h domain from human smubp-2
82 | d1msza_ |
| not modelled | 7.3 | 21 | Fold:IF3-like Superfamily:R3H domain Family:R3H domain
83 | c2vn1A_ |
| not modelled | 7.1 | 13 | PDB header:isomerase Chain: A: PDB Molecule:70 kda peptidylprolyl isomerase; PDBTitle: crystal structure of the fk506-binding domain of plasmodium2 falciparum fkbp35 in complex with fk506
84 | d1cgla_ |
| not modelled | 7.0 | 22 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Matrix metalloproteases, catalytic domain
85 | c3lfmA_ |
| not modelled | 7.0 | 46 | PDB header:oxidoreductase Chain: A: PDB Molecule:protein fto; PDBTitle: crystal structure of the fat mass and obesity associated (fto) protein2 reveals basis for its substrate specificity
86 | d1bqqm_ |
| not modelled | 7.0 | 32 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Matrix metalloproteases, catalytic domain
87 | d1g0da2 |
| not modelled | 6.8 | 21 | Fold:Immunoglobulin-like beta-sandwich Superfamily:Transglutaminase, two C-terminal domains Family:Transglutaminase, two C-terminal domains
88 | d1nmpa_ |
| not modelled | 6.7 | 6 | Fold:NIF3 (NGG1p interacting factor 3)-like Superfamily:NIF3 (NGG1p interacting factor 3)-like Family:NIF3 (NGG1p interacting factor 3)-like
89 | d2fg9a1 |
| not modelled | 6.6 | 19 | Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like
90 | d1s1qa_ |
| not modelled | 6.6 | 18 | Fold:UBC-like Superfamily:UBC-like Family:UEV domain
91 | c3eytA_ |
| not modelled | 6.6 | 24 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein spoa0173; PDBTitle: crystal structure of thioredoxin-like superfamily protein spoa0173
92 | c2e1cA_ |
| not modelled | 6.4 | 16 | PDB header:transcription/dna Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519; PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
93 | d2ovxa1 |
| not modelled | 6.2 | 22 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Matrix metalloproteases, catalytic domain
94 | d2b5xa1 |
| not modelled | 6.2 | 15 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
95 | c2obiA_ |
| not modelled | 6.1 | 15 | PDB header:oxidoreductase Chain: A: PDB Molecule:phospholipid hydroperoxide glutathione PDBTitle: crystal structure of the selenocysteine to cysteine mutant2 of human phospholipid hydroperoxide glutathione peroxidase3 (gpx4)
96 | d1nkva_ |
| not modelled | 6.0 | 8 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Hypothetical Protein YjhP
97 | d1r9ha_ |
| not modelled | 5.8 | 16 | Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase
98 | c2l4bA_ |
| not modelled | 5.7 | 24 | PDB header:transferase Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: solution structure of a putative acyl carrier protein from anaplasma2 phagocytophilum. seattle structural genomics center for infectious3 disease target anpha.01018.a
99 | c3iz6D_ |
| not modelled | 5.7 | 14 | PDB header:ribosome Chain: D: PDB Molecule:40s ribosomal protein s4 (s4e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

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