Phyre 2 Results for P21365

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Email | l.a.kelley@imperial.ac.uk
Description | P21365
Date | Thu Jan 5 11:38:11 GMT 2012
Unique Job ID | 2a8dc698076db141

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2kvlA_
Top template information
PDB header:viral protein Chain: A: PDB Molecule:major outer capsid protein vp7; PDBTitle: nmr structure of the c-terminal domain of vp7
Confidence and coverage
Confidence: | 23.2% | Coverage: | 8%
19 residues ( 8% of your sequence) have been modelled with 23.2% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | S | I | T | A | Q | S | V | Y | R | D | T | G | N | F | F | R | N | Q | F | M | T | I | L | L | V | S | L | L | C | A | F | I | T | V | V | L | G | H | V | F | S | P | S | D | A | Q | L | A | Q | L | N | D | G | V | P | V | S | G | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | G | L | F | D | L | V | Q | N | M | S | P | E | Q | Q | Q | I | L | L | Q | A | S | A | A | S | T | F | S | G | L | I | G | N | A | I | L | A | G | G | V | I | L | I | I | Q | L | V | S | A | G | Q | R | V | S | A | L | R | A | I | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? | ? | ? | ? |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | A | S | A | P | I | L | P | K | L | F | I | L | I | F | L | T | T | L | L | V | Q | I | G | I | M | L | V | V | V | P | G | I | I | M | A | I | L | L | A | L | A | P | V | M | L | V | Q | D | K | M | G | V | F | A | S | M | R | S | S | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | R | L | T | W | A | N | M | R | L | V | A | P | A | V | L | S | W | L | L | A | K | T | L | L | L | L | F | A | S | S | F | A | A | L | T | P | E | I | G | A | V | L | A | N | T | L | S | N | L | I | S | A | I | L | L | I | Y | L | F | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | .
Sequence |  | L | Y | M | L | I | R | Q
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 |
| c2kvlA_ |

### PDB 2kvl chain A

Region: 177 - 195
Aligned: 19
Modelled: 19
Confidence: 23.2%
Identity: 26%
PDB header:viral protein
Chain: A: PDB Molecule:major outer capsid protein vp7;
PDBTitle: nmr structure of the c-terminal domain of vp7

Phyre2
2 |
| c3hd7A_ |

### PDB 3hd7 chain A

Region: 177 - 212
Aligned: 36
Modelled: 36
Confidence: 17.8%
Identity: 8%
PDB header:exocytosis
Chain: A: PDB Molecule:vesicle-associated membrane protein 2;
PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1

Phyre2
3 |
| c1ciiA_ |

### PDB 1cii chain A

Region: 185 - 234
Aligned: 50
Modelled: 50
Confidence: 13.5%
Identity: 18%
PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia

Phyre2
4 |
| d1k8rb_ |

### PDB 1k8r chain B

Region: 173 - 182
Aligned: 10
Modelled: 10
Confidence: 9.5%
Identity: 30%
Fold: beta-Grasp (ubiquitin-like)
Superfamily: Ubiquitin-like
Family: Ras-binding domain, RBD

Phyre2
5 |
| d2hgca1 |

### PDB 2hgc chain A domain 1

Region: 6 - 19
Aligned: 14
Modelled: 14
Confidence: 9.0%
Identity: 21%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: YjcQ-like

Phyre2
6 |
| c2hgcA_ |

### PDB 2hgc chain A

Region: 6 - 19
Aligned: 14
Modelled: 14
Confidence: 9.0%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:yjcq protein;
PDBTitle: solution nmr structure of the yjcq protein from bacillus2 subtilis. northeast structural genomics target sr346.

Phyre2
7 |
| d1k8ke_ |

### PDB 1k8k chain E

Region: 7 - 19
Aligned: 13
Modelled: 13
Confidence: 8.7%
Identity: 8%
Fold: Arp2/3 complex 21 kDa subunit ARPC3
Superfamily: Arp2/3 complex 21 kDa subunit ARPC3
Family: Arp2/3 complex 21 kDa subunit ARPC3

Phyre2
8 |
| c1rh5C_ |

### PDB 1rh5 chain C

Region: 11 - 39
Aligned: 29
Modelled: 29
Confidence: 8.6%
Identity: 17%
PDB header:protein transport
Chain: C: PDB Molecule:secbeta;
PDBTitle: the structure of a protein conducting channel

Phyre2
9 |
| d1rh5c_ |

### PDB 1rh5 chain C

Region: 11 - 39
Aligned: 29
Modelled: 29
Confidence: 8.6%
Identity: 17%
Fold: Single transmembrane helix
Superfamily: Sec-beta subunit
Family: Sec-beta subunit

Phyre2
10 |
| c3go5A_ |

### PDB 3go5 chain A

Region: 167 - 195
Aligned: 29
Modelled: 28
Confidence: 8.2%
Identity: 0%
PDB header:gene regulation
Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains;
PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution

Phyre2
11 |
| d1pf4a2 |

### PDB 1pf4 chain A domain 2

Region: 173 - 216
Aligned: 44
Modelled: 44
Confidence: 8.2%
Identity: 5%
Fold: ABC transporter transmembrane region
Superfamily: ABC transporter transmembrane region
Family: ABC transporter transmembrane region

Phyre2
12 |
| c1m45B_ |

### PDB 1m45 chain B

Region: 9 - 24
Aligned: 16
Modelled: 16
Confidence: 8.2%
Identity: 6%
PDB header:cell cycle protein
Chain: B: PDB Molecule:iq2 motif from myo2p, a class v myosin;
PDBTitle: crystal structure of mlc1p bound to iq2 of myo2p, a class v2 myosin

Phyre2
13 |
| c1q2iA_ |

### PDB 1q2i chain A

Region: 176 - 188
Aligned: 13
Modelled: 13
Confidence: 7.7%
Identity: 0%
PDB header:antitumor protein
Chain: A: PDB Molecule:pnc27;
PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells

Phyre2
14 |
| c1unhD_ |

### PDB 1unh chain D

Region: 241 - 247
Aligned: 7
Modelled: 7
Confidence: 7.4%
Identity: 71%
PDB header:cell cycle
Chain: D: PDB Molecule:cyclin-dependent kinase 5 activator 1;
PDBTitle: structural mechanism for the inhibition of cdk5-p25 by2 roscovitine, aloisine and indirubin.

Phyre2
15 |
| d1unld_ |

### PDB 1unl chain D

Region: 241 - 247
Aligned: 7
Modelled: 7
Confidence: 7.4%
Identity: 71%
Fold: Cyclin-like
Superfamily: Cyclin-like
Family: Cyclin

Phyre2
16 |
| c1kq8A_ |

### PDB 1kq8 chain A

Region: 97 - 127
Aligned: 31
Modelled: 31
Confidence: 7.3%
Identity: 19%
PDB header:transcription
Chain: A: PDB Molecule:hepatocyte nuclear factor 3 forkhead homolog 1;
PDBTitle: solution structure of winged helix protein hfh-1

Phyre2
17 |
| d1kq8a_ |

### PDB 1kq8 chain A

Region: 97 - 127
Aligned: 31
Modelled: 31
Confidence: 7.3%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Forkhead DNA-binding domain

Phyre2
18 |
| c3jqoV_ |

### PDB 3jqo chain V

Region: 183 - 201
Aligned: 19
Modelled: 14
Confidence: 7.0%
Identity: 11%
PDB header:transport protein
Chain: V: PDB Molecule:traf protein;
PDBTitle: crystal structure of the outer membrane complex of a type iv2 secretion system

Phyre2
19 |
| c4a1aM_ |

### PDB 4a1a chain M

Region: 2 - 20
Aligned: 19
Modelled: 19
Confidence: 7.0%
Identity: 5%
PDB header:ribosome
Chain: M: PDB Molecule:60s ribosomal protein l5;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3.

Phyre2
20 |
| c1zp0D_ |

### PDB 1zp0 chain D

Region: 151 - 182
Aligned: 32
Modelled: 32
Confidence: 6.9%
Identity: 13%
PDB header:oxidoreductase
Chain: D: PDB Molecule:small cytochrome binding protein;
PDBTitle: crystal structure of mitochondrial respiratory complex ii2 bound with 3-nitropropionate and 2-thenoyltrifluoroacetone

Phyre2
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22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2kvlA_ |
|  | 23.2 | 26 | PDB header:viral protein Chain: A: PDB Molecule:major outer capsid protein vp7; PDBTitle: nmr structure of the c-terminal domain of vp7
2 | c3hd7A_ |
|  | 17.8 | 8 | PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1
3 | c1ciiA_ |
|  | 13.5 | 18 | PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia
4 | d1k8rb_ |
|  | 9.5 | 30 | Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD
5 | d2hgca1 |
|  | 9.0 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:YjcQ-like
6 | c2hgcA_ |
|  | 9.0 | 21 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yjcq protein; PDBTitle: solution nmr structure of the yjcq protein from bacillus2 subtilis. northeast structural genomics target sr346.
7 | d1k8ke_ |
|  | 8.7 | 8 | Fold:Arp2/3 complex 21 kDa subunit ARPC3 Superfamily:Arp2/3 complex 21 kDa subunit ARPC3 Family:Arp2/3 complex 21 kDa subunit ARPC3
8 | c1rh5C_ |
|  | 8.6 | 17 | PDB header:protein transport Chain: C: PDB Molecule:secbeta; PDBTitle: the structure of a protein conducting channel
9 | d1rh5c_ |
|  | 8.6 | 17 | Fold:Single transmembrane helix Superfamily:Sec-beta subunit Family:Sec-beta subunit
10 | c3go5A_ |
|  | 8.2 | 0 | PDB header:gene regulation Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains; PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution
11 | d1pf4a2 |
|  | 8.2 | 5 | Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region
12 | c1m45B_ |
|  | 8.2 | 6 | PDB header:cell cycle protein Chain: B: PDB Molecule:iq2 motif from myo2p, a class v myosin; PDBTitle: crystal structure of mlc1p bound to iq2 of myo2p, a class v2 myosin
13 | c1q2iA_ |
|  | 7.7 | 0 | PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells
14 | c1unhD_ |
|  | 7.4 | 71 | PDB header:cell cycle Chain: D: PDB Molecule:cyclin-dependent kinase 5 activator 1; PDBTitle: structural mechanism for the inhibition of cdk5-p25 by2 roscovitine, aloisine and indirubin.
15 | d1unld_ |
|  | 7.4 | 71 | Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin
16 | c1kq8A_ |
|  | 7.3 | 19 | PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 3 forkhead homolog 1; PDBTitle: solution structure of winged helix protein hfh-1
17 | d1kq8a_ |
|  | 7.3 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain
18 | c3jqoV_ |
|  | 7.0 | 11 | PDB header:transport protein Chain: V: PDB Molecule:traf protein; PDBTitle: crystal structure of the outer membrane complex of a type iv2 secretion system
19 | c4a1aM_ |
|  | 7.0 | 5 | PDB header:ribosome Chain: M: PDB Molecule:60s ribosomal protein l5; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3.
20 | c1zp0D_ |
|  | 6.9 | 13 | PDB header:oxidoreductase Chain: D: PDB Molecule:small cytochrome binding protein; PDBTitle: crystal structure of mitochondrial respiratory complex ii2 bound with 3-nitropropionate and 2-thenoyltrifluoroacetone
21 | d1cg5a_ |
| not modelled | 6.8 | 21 | Fold:Globin-like Superfamily:Globin-like Family:Globins
22 | c3mkuA_ |
| not modelled | 6.6 | 13 | PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter
23 | c1e17A_ |
| not modelled | 6.4 | 10 | PDB header:dna binding domain Chain: A: PDB Molecule:afx; PDBTitle: solution structure of the dna binding domain of the human2 forkhead transcription factor afx (foxo4)
24 | c3co7C_ |
| not modelled | 6.2 | 16 | PDB header:transcription/dna Chain: C: PDB Molecule:forkhead box protein o1; PDBTitle: crystal structure of foxo1 dbd bound to dbe2 dna
25 | d1myta_ |
| not modelled | 6.2 | 19 | Fold:Globin-like Superfamily:Globin-like Family:Globins
26 | d2fx0a2 |
| not modelled | 6.1 | 0 | Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain
27 | d1hdsa_ |
| not modelled | 6.1 | 7 | Fold:Globin-like Superfamily:Globin-like Family:Globins
28 | c2lkeA_ |
| not modelled | 5.9 | 30 | PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-m; PDBTitle: structures and interaction analyses of the integrin alpha-m beta-22 cytoplasmic tails
29 | c3g73A_ |
| not modelled | 5.9 | 10 | PDB header:transcription/dna Chain: A: PDB Molecule:forkhead box protein m1; PDBTitle: structure of the foxm1 dna binding
30 | c1geaA_ |
| not modelled | 5.9 | 25 | PDB header:neuropeptide Chain: A: PDB Molecule:pituitary adenylate cyclase activating PDBTitle: receptor-bound conformation of pacap21
31 | c2ciuA_ |
| not modelled | 5.9 | 0 | PDB header:protein transport Chain: A: PDB Molecule:import inner membrane translocase subunit tim21 PDBTitle: structure of the ims domain of the mitochondrial import2 protein tim21 from s. cerevisiae
32 | c1n2dC_ |
| not modelled | 5.8 | 6 | PDB header:cell cycle Chain: C: PDB Molecule:iq2 and iq3 motifs from myo2p, a class v myosin; PDBTitle: ternary complex of mlc1p bound to iq2 and iq3 of myo2p, a2 class v myosin
33 | c2lkjA_ |
| not modelled | 5.6 | 33 | PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-m; PDBTitle: structures and interaction analyses of the integrin alpha-m beta-22 cytoplasmic tails
34 | d2lhba_ |
| not modelled | 5.6 | 7 | Fold:Globin-like Superfamily:Globin-like Family:Globins
35 | d1d5va_ |
| not modelled | 5.6 | 6 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain
36 | c2wwbB_ |
| not modelled | 5.6 | 7 | PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome
37 | c2rlwA_ |
| not modelled | 5.6 | 14 | PDB header:toxin Chain: A: PDB Molecule:plnf; PDBTitle: three-dimensional structure of the two peptides that2 constitute the two-peptide bacteriocin plantaracin ef
38 | c2qq4A_ |
| not modelled | 5.5 | 20 | PDB header:metal binding protein Chain: A: PDB Molecule:iron-sulfur cluster biosynthesis protein iscu; PDBTitle: crystal structure of iron-sulfur cluster biosynthesis2 protein iscu (ttha1736) from thermus thermophilus hb8
39 | c1yhuW_ |
| not modelled | 5.5 | 14 | PDB header:oxygen storage/transport Chain: W: PDB Molecule:hemoglobin b1a chain; PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits.
40 | d3bpya1 |
| not modelled | 5.5 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain
41 | d1scta_ |
| not modelled | 5.5 | 23 | Fold:Globin-like Superfamily:Globin-like Family:Globins
42 | d2hfha_ |
| not modelled | 5.4 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain
43 | c2zs1D_ |
| not modelled | 5.4 | 8 | PDB header:oxygen storage, oxygen transport Chain: D: PDB Molecule:extracellular giant hemoglobin major globin subunit b1; PDBTitle: structural basis for the heterotropic and homotropic interactions of2 invertebrate giant hemoglobin
44 | d1sxja1 |
| not modelled | 5.4 | 9 | Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain
45 | d1c17m_ |
| not modelled | 5.4 | 11 | Fold:F1F0 ATP synthase subunit A Superfamily:F1F0 ATP synthase subunit A Family:F1F0 ATP synthase subunit A
46 | c1g2cN_ |
| not modelled | 5.3 | 13 | PDB header:viral protein Chain: N: PDB Molecule:fusion protein (f); PDBTitle: human respiratory syncytial virus fusion protein core
47 | d2a07f1 |
| not modelled | 5.3 | 6 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain
48 | c2wukD_ |
| not modelled | 5.3 | 17 | PDB header:cell cycle Chain: D: PDB Molecule:septum site-determining protein diviva; PDBTitle: diviva n-terminal domain, f17a mutant
49 | c2nq2A_ |
| not modelled | 5.3 | 16 | PDB header:metal transport Chain: A: PDB Molecule:hypothetical abc transporter permease protein PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter.
50 | d1hbra_ |
| not modelled | 5.3 | 0 | Fold:Globin-like Superfamily:Globin-like Family:Globins
51 | c2c0kB_ |
| not modelled | 5.3 | 11 | PDB header:oxygen transport Chain: B: PDB Molecule:hemoglobin; PDBTitle: the structure of hemoglobin from the botfly gasterophilus2 intestinalis
52 | c3gztF_ |
| not modelled | 5.2 | 28 | PDB header:virus Chain: F: PDB Molecule:outer capsid glycoprotein vp7; PDBTitle: vp7 recoated rotavirus dlp
53 | c3bjqA_ |
| not modelled | 5.2 | 14 | PDB header:viral protein Chain: A: PDB Molecule:phage-related protein; PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution
54 | d2gdma_ |
| not modelled | 5.2 | 9 | Fold:Globin-like Superfamily:Globin-like Family:Globins
55 | c3h8aF_ |
| not modelled | 5.1 | 40 | PDB header:lyase/protein binding Chain: F: PDB Molecule:rnase e; PDBTitle: crystal structure of e. coli enolase bound to its cognate rnase e2 recognition domain

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