Phyre 2 Results for P37675

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Email | l.a.kelley@imperial.ac.uk
Description | P37675
Date | Thu Jan 5 11:56:49 GMT 2012
Unique Job ID | c134bca4058c2675

Summary |

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

Model (left) based on template c3qnqD_
Top template information
PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
Confidence and coverage
Confidence: | 51.8% | Coverage: | 31%
131 residues ( 31% of your sequence) have been modelled with 51.8% confidence by the single highest scoring template.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | A | V | L | I | F | L | G | C | L | L | G | G | I | A | I | G | L | P | I | A | W | A | L | L | L | C | G | A | A | L | M | F | W | L | D | M | F | D | V | Q | I | M | A | Q | T | L | V | N | G | A | D | S | F | S | L | L | A | I | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | F | F | V | L | A | G | E | I | M | N | A | G | G | L | S | K | R | I | V | D | L | P | M | K | L | V | G | H | K | P | G | G | L | G | Y | V | G | V | L | A | A | M | I | M | A | S | L | S | G | S | A | V | A | D | T | A | A | V | A | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | L | L | V | P | M | M | R | S | A | N | Y | P | V | N | R | A | A | G | L | I | A | S | G | G | I | I | A | P | I | I | P | P | S | I | P | F | I | I | F | G | V | S | S | G | L | S | I | S | K | L | F | M | A | G | I | A | P | G | M | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | M | G | A | T | L | M | L | T | W | W | W | Q | A | S | R | L | N | L | P | R | Q | Q | K | A | T | M | Q | E | I | W | H | S | F | V | S | G | I | W | A | L | F | L | P | V | I | I | I | G | G | F | R | S | G | L | F | T | P | T | E | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | G | A | V | A | A | F | Y | A | L | F | V | A | T | V | I | Y | R | E | M | T | F | A | T | L | W | H | V | L | I | G | A | A | K | T | T | S | V | V | M | F | L | V | A | S | A | Q | V | S | A | W | L | I | T | I | A | E | L | P | M | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | . | . | . | . | . | 360
Sequence |  | V | S | D | L | L | Q | P | L | V | D | S | P | R | L | L | F | I | V | I | M | V | A | I | L | I | V | G | M | V | M | D | L | T | P | T | V | L | I | L | T | P | V | L | M | P | L | V | K | E | A | G | I | D | P | I | Y | F | G | V | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 370 | . | . | . | . | . | . | . | . | . | 380 | . | . | . | . | . | . | . | . | . | 390 | . | . | . | . | . | . | . | . | . | 400 | . | . | . | . | . | . | . | . | . | 410 | . | . | . | . | . | . | . | . | . | 420
Sequence |  | F | I | I | N | C | S | I | G | L | I | T | P | P | I | G | N | V | L | N | V | I | S | G | V | A | K | L | K | F | D | D | A | V | R | G | V | F | P | Y | V | L | V | L | Y | S | L | L | V | V | F | V | F | I | P | D | L | I | I | L | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | .
Sequence |  | L | K | W | I | N
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 |
| c3qnqD_ |

### PDB 3qnq chain D

Region: 78 - 208
Aligned: 131
Modelled: 131
Confidence: 51.8%
Identity: 7%
PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system

Phyre2
2 |
| d1y5ic1 |

### PDB 1y5i chain C domain 1

Region: 166 - 307
Aligned: 142
Modelled: 142
Confidence: 30.0%
Identity: 11%
Fold: Heme-binding four-helical bundle
Superfamily: Respiratory nitrate reductase 1 gamma chain
Family: Respiratory nitrate reductase 1 gamma chain

Phyre2
3 |
| d1fftb2 |

### PDB 1fft chain B domain 2

Region: 170 - 236
Aligned: 67
Modelled: 67
Confidence: 18.7%
Identity: 10%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2
4 |
| c2w8aC_ |

### PDB 2w8a chain C

Region: 27 - 218
Aligned: 180
Modelled: 191
Confidence: 17.8%
Identity: 13%
PDB header:membrane protein
Chain: C: PDB Molecule:glycine betaine transporter betp;
PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate

Phyre2
5 |
| c2bbjB_ |

### PDB 2bbj chain B

Region: 155 - 197
Aligned: 40
Modelled: 43
Confidence: 17.4%
Identity: 8%
PDB header:metal transport/membrane protein
Chain: B: PDB Molecule:divalent cation transport-related protein;
PDBTitle: crystal structure of the cora mg2+ transporter

Phyre2
6 |
| c2kncA_ |

### PDB 2knc chain A

Region: 164 - 209
Aligned: 46
Modelled: 46
Confidence: 14.0%
Identity: 9%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2
7 |
| c2rddB_ |

### PDB 2rdd chain B

Region: 174 - 202
Aligned: 29
Modelled: 29
Confidence: 13.4%
Identity: 7%
PDB header:membrane protein/transport protein
Chain: B: PDB Molecule:upf0092 membrane protein yajc;
PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.

Phyre2
8 |
| c2xq2A_ |

### PDB 2xq2 chain A

Region: 10 - 256
Aligned: 234
Modelled: 234
Confidence: 13.2%
Identity: 10%
PDB header:transport protein
Chain: A: PDB Molecule:sodium/glucose cotransporter;
PDBTitle: structure of the k294a mutant of vsglt

Phyre2
9 |
| c2xutC_ |

### PDB 2xut chain C

Region: 63 - 219
Aligned: 157
Modelled: 157
Confidence: 13.0%
Identity: 4%
PDB header:transport protein
Chain: C: PDB Molecule:proton/peptide symporter family protein;
PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter.

Phyre2
10 |
| d2oara1 |

### PDB 2oar chain A domain 1

Region: 165 - 210
Aligned: 46
Modelled: 46
Confidence: 12.6%
Identity: 11%
Fold: Gated mechanosensitive channel
Superfamily: Gated mechanosensitive channel
Family: Gated mechanosensitive channel

Phyre2
11 |
| c2jlnA_ |

### PDB 2jln chain A

Region: 174 - 212
Aligned: 39
Modelled: 39
Confidence: 12.2%
Identity: 8%
PDB header:membrane protein
Chain: A: PDB Molecule:mhp1;
PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter

Phyre2
12 |
| d1j4na_ |

### PDB 1j4n chain A

Region: 134 - 206
Aligned: 73
Modelled: 73
Confidence: 12.1%
Identity: 7%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

Phyre2
13 |
| d1u5ta1 |

### PDB 1u5t chain A domain 1

Region: 343 - 356
Aligned: 14
Modelled: 14
Confidence: 12.1%
Identity: 36%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Vacuolar sorting protein domain

Phyre2
14 |
| c3mk7F_ |

### PDB 3mk7 chain F

Region: 170 - 235
Aligned: 66
Modelled: 66
Confidence: 11.8%
Identity: 8%
PDB header:oxidoreductase
Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p;
PDBTitle: the structure of cbb3 cytochrome oxidase

Phyre2
15 |
| d3ehbb2 |

### PDB 3ehb chain B domain 2

Region: 167 - 236
Aligned: 70
Modelled: 70
Confidence: 10.8%
Identity: 13%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2
16 |
| c1vryA_ |

### PDB 1vry chain A

Region: 18 - 70
Aligned: 51
Modelled: 53
Confidence: 10.4%
Identity: 12%
PDB header:membrane protein
Chain: A: PDB Molecule:glycine receptor alpha-1 chain;
PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor

Phyre2
17 |
| c1m57H_ |

### PDB 1m57 chain H

Region: 167 - 233
Aligned: 67
Modelled: 67
Confidence: 9.9%
Identity: 12%
PDB header:oxidoreductase
Chain: H: PDB Molecule:cytochrome c oxidase;
PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant))

Phyre2
18 |
| d3dtub2 |

### PDB 3dtu chain B domain 2

Region: 167 - 236
Aligned: 70
Modelled: 70
Confidence: 9.6%
Identity: 11%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2
19 |
| c1ymgA_ |

### PDB 1ymg chain A

Region: 103 - 207
Aligned: 105
Modelled: 105
Confidence: 9.0%
Identity: 9%
PDB header:membrane protein
Chain: A: PDB Molecule:lens fiber major intrinsic protein;
PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution

Phyre2
20 |
| d1ymga1 |

### PDB 1ymg chain A domain 1

Region: 103 - 207
Aligned: 105
Modelled: 105
Confidence: 9.0%
Identity: 9%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

Phyre2
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74 |
75 |
76 |
77 |
78 |
79 |
80 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3qnqD_ |
|  | 51.8 | 7 | PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
2 | d1y5ic1 |
|  | 30.0 | 11 | Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain
3 | d1fftb2 |
|  | 18.7 | 10 | Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region
4 | c2w8aC_ |
|  | 17.8 | 13 | PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate
5 | c2bbjB_ |
|  | 17.4 | 8 | PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter
6 | c2kncA_ |
|  | 14.0 | 9 | PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
7 | c2rddB_ |
|  | 13.4 | 7 | PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.
8 | c2xq2A_ |
|  | 13.2 | 10 | PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt
9 | c2xutC_ |
|  | 13.0 | 4 | PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter.
10 | d2oara1 |
|  | 12.6 | 11 | Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel
11 | c2jlnA_ |
|  | 12.2 | 8 | PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter
12 | d1j4na_ |
|  | 12.1 | 7 | Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like
13 | d1u5ta1 |
|  | 12.1 | 36 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain
14 | c3mk7F_ |
|  | 11.8 | 8 | PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase
15 | d3ehbb2 |
|  | 10.8 | 13 | Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region
16 | c1vryA_ |
|  | 10.4 | 12 | PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor
17 | c1m57H_ |
|  | 9.9 | 12 | PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant))
18 | d3dtub2 |
|  | 9.6 | 11 | Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region
19 | c1ymgA_ |
|  | 9.0 | 9 | PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution
20 | d1ymga1 |
|  | 9.0 | 9 | Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like
21 | c1fftG_ |
| not modelled | 8.9 | 12 | PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli
22 | c2kncB_ |
| not modelled | 8.8 | 16 | PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
23 | d1bg6a1 |
| not modelled | 8.8 | 21 | Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:N-(1-D-carboxylethyl)-L-norvaline dehydrogenase
24 | d1o82a_ |
| not modelled | 8.7 | 22 | Fold:Saposin-like Superfamily:Bacteriocin AS-48 Family:Bacteriocin AS-48
25 | c1qleB_ |
| not modelled | 8.5 | 13 | PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment
26 | c1ar1B_ |
| not modelled | 8.5 | 13 | PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment
27 | c3cuqA_ |
| not modelled | 8.5 | 23 | PDB header:protein transport Chain: A: PDB Molecule:vacuolar-sorting protein snf8; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex
28 | c1u5tA_ |
| not modelled | 8.3 | 36 | PDB header:transport protein Chain: A: PDB Molecule:appears to be functionally related to snf7; PDBTitle: structure of the escrt-ii endosomal trafficking complex
29 | c2zmeA_ |
| not modelled | 8.1 | 23 | PDB header:protein transport Chain: A: PDB Molecule:vacuolar-sorting protein snf8; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex
30 | c3si5X_ |
| not modelled | 8.1 | 30 | PDB header:cell cycle Chain: X: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex
31 | c3si5Y_ |
| not modelled | 7.9 | 30 | PDB header:cell cycle Chain: Y: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex
32 | d1mmsa2 |
| not modelled | 7.8 | 19 | Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain
33 | d2d6fc1 |
| not modelled | 7.7 | 33 | Fold:GatB/YqeY motif Superfamily:GatB/YqeY motif Family:GatB/GatE C-terminal domain-like
34 | d3cjsb1 |
| not modelled | 7.6 | 24 | Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain
35 | d1rc2a_ |
| not modelled | 7.5 | 10 | Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like
36 | c2oarA_ |
| not modelled | 7.4 | 4 | PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl)
37 | c2ksfA_ |
| not modelled | 7.2 | 15 | PDB header:transferase Chain: A: PDB Molecule:sensor protein kdpd; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor kdpd, center for structures of3 membrane proteins (csmp) target 4312c
38 | d2iuba2 |
| not modelled | 7.2 | 4 | Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region
39 | d1eysh2 |
| not modelled | 7.1 | 20 | Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region
40 | c3rkoM_ |
| not modelled | 7.0 | 8 | PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution
41 | c3cjtP_ |
| not modelled | 6.9 | 24 | PDB header:transferase/ribosomal protein Chain: P: PDB Molecule:50s ribosomal protein l11; PDBTitle: ribosomal protein l11 methyltransferase (prma) in complex with2 dimethylated ribosomal protein l11
42 | c2l2tA_ |
| not modelled | 6.8 | 21 | PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain
43 | c3ke2A_ |
| not modelled | 6.8 | 9 | PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein yp_928783.1; PDBTitle: crystal structure of a duf2131 family protein (sama_2911) from2 shewanella amazonensis sb2b at 2.50 a resolution
44 | d2a65a1 |
| not modelled | 6.7 | 9 | Fold:SNF-like Superfamily:SNF-like Family:SNF-like
45 | d1tm9a_ |
| not modelled | 6.6 | 14 | Fold:Hypothetical protein MG354 Superfamily:Hypothetical protein MG354 Family:Hypothetical protein MG354
46 | c1c9bI_ |
| not modelled | 6.4 | 22 | PDB header:transcription/dna Chain: I: PDB Molecule:general transcription factor iib; PDBTitle: crystal structure of a human tbp core domain-human tfiib2 core domain complex bound to an extended, modified3 adenoviral major late promoter (admlp)
47 | c1s5rA_ |
| not modelled | 6.3 | 31 | PDB header:transcription Chain: A: PDB Molecule:high mobility group box transcription factor 1; PDBTitle: solution structure of hbp1 sid-msin3a pah2 complex
48 | d2vv5a3 |
| not modelled | 6.2 | 5 | Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region
49 | d2csba3 |
| not modelled | 6.2 | 13 | Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain
50 | c3gdzA_ |
| not modelled | 6.1 | 17 | PDB header:ligase Chain: A: PDB Molecule:arginyl-trna synthetase; PDBTitle: crystal structure of arginyl-trna synthetase from klebsiella2 pneumoniae subsp. pneumoniae
51 | c3kl4B_ |
| not modelled | 6.1 | 15 | PDB header:hydrolase Chain: B: PDB Molecule:signal peptide of yeast dipeptidyl aminopeptidase b; PDBTitle: recognition of a signal peptide by the signal recognition particle
52 | c1ponB_ |
| not modelled | 6.0 | 18 | PDB header:calcium-binding protein Chain: B: PDB Molecule:troponin c; PDBTitle: site iii-site iv troponin c heterodimer, nmr
53 | c3rfrI_ |
| not modelled | 5.9 | 3 | PDB header:oxidoreductase Chain: I: PDB Molecule:pmob; PDBTitle: crystal structure of particulate methane monooxygenase (pmmo) from2 methylocystis sp. strain m
54 | c2kluA_ |
| not modelled | 5.8 | 9 | PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4
55 | d2h8aa1 |
| not modelled | 5.7 | 14 | Fold:MAPEG domain-like Superfamily:MAPEG domain-like Family:MAPEG domain
56 | c2k6oA_ |
| not modelled | 5.6 | 27 | PDB header:antimicrobial protein Chain: A: PDB Molecule:cathelicidin antimicrobial peptide; PDBTitle: human ll-37 structure
57 | d2pp6a1 |
| not modelled | 5.6 | 24 | Fold:Phage tail proteins Superfamily:Phage tail proteins Family:gpFII-like
58 | c1tr8A_ |
| not modelled | 5.6 | 19 | PDB header:chaperone Chain: A: PDB Molecule:conserved protein (mth177); PDBTitle: crystal structure of archaeal nascent polypeptide-associated complex2 (aenac)
59 | d1nera_ |
| not modelled | 5.5 | 8 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
60 | d1vola2 |
| not modelled | 5.5 | 22 | Fold:Cyclin-like Superfamily:Cyclin-like Family:Transcription factor IIB (TFIIB), core domain
61 | d2bnma1 |
| not modelled | 5.4 | 41 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
62 | d1rzsa_ |
| not modelled | 5.4 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
63 | c1s6cB_ |
| not modelled | 5.4 | 0 | PDB header:transport protein Chain: B: PDB Molecule:potassium voltage-gated channel subfamily d member 2; PDBTitle: crystal structure of the complex between kchip1 and kv4.2 n1-30
64 | c1yewC_ |
| not modelled | 5.4 | 10 | PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase
65 | c2dalA_ |
| not modelled | 5.4 | 12 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein kiaa0794; PDBTitle: solution structure of the novel identified uba-like domain2 in the n-terminal of human fas associated factor 1 protein
66 | d1gyxa_ |
| not modelled | 5.3 | 17 | Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like
67 | c2op8A_ |
| not modelled | 5.3 | 8 | PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase ywhb; PDBTitle: crystal structure of ywhb- homologue of 4-oxalocrotonate tautomerase
68 | d1v92a_ |
| not modelled | 5.2 | 13 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:TAP-C domain-like
69 | d1khia2 |
| not modelled | 5.2 | 14 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
70 | d1xmta_ |
| not modelled | 5.2 | 10 | Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-acetyl transferase, NAT
71 | c3rgbA_ |
| not modelled | 5.2 | 4 | PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath)
72 | d1dwka1 |
| not modelled | 5.2 | 5 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Cyanase N-terminal domain
73 | c2vv5D_ |
| not modelled | 5.1 | 8 | PDB header:membrane protein Chain: D: PDB Molecule:small-conductance mechanosensitive channel; PDBTitle: the open structure of mscs
74 | d1qd1a2 |
| not modelled | 5.1 | 17 | Fold:Ferredoxin-like Superfamily:Formiminotransferase domain of formiminotransferase-cyclodeaminase. Family:Formiminotransferase domain of formiminotransferase-cyclodeaminase.
75 | c2jp3A_ |
| not modelled | 5.1 | 7 | PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles
76 | c1kftA_ |
| not modelled | 5.1 | 19 | PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli
77 | d1kfta_ |
| not modelled | 5.1 | 19 | Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain
78 | c2g9pA_ |
| not modelled | 5.1 | 25 | PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom
79 | c2bg9C_ |
| not modelled | 5.1 | 13 | PDB header:ion channel/receptor Chain: C: PDB Molecule:acetylcholine receptor protein, delta chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution.
80 | c1bvyF_ |
| not modelled | 5.0 | 10 | PDB header:oxidoreductase Chain: F: PDB Molecule:protein (cytochrome p450 bm-3); PDBTitle: complex of the heme and fmn-binding domains of the2 cytochrome p450(bm-3)

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