Phyre 2 Results for P38392

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Email | l.a.kelley@imperial.ac.uk
Description | P38392
Date | Thu Jan 5 11:58:06 GMT 2012
Unique Job ID | 32ae6d22fe9febba

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c1htrP_
Top template information
PDB header:aspartyl protease Chain: P: PDB Molecule:progastricsin (pro segment); PDBTitle: crystal and molecular structures of human progastricsin at 1.622 angstroms resolution
Confidence and coverage
Confidence: | 46.3% | Coverage: | 17%
27 residues ( 17% of your sequence) have been modelled with 46.3% 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 | L | D | V | F | T | P | L | L | K | L | F | A | N | E | P | L | E | R | L | M | Y | T | I | I | I | F | G | L | T | L | W | L | I | P | K | E | F | T | V | A | F | N | A | Y | T | E | I | P | W | L | F | Q | I | I | V | F | A | F | S
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SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | F | V | V | A | I | S | F | S | R | L | R | A | H | I | Q | K | H | Y | S | L | L | P | E | Q | R | V | L | L | R | L | S | E | K | E | I | A | V | F | K | D | F | L | K | T | G | N | L | I | I | T | S | P | C | R | N | P | V | M | K | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | .
Sequence |  | L | E | R | K | G | I | I | Q | H | Q | S | D | S | A | N | C | S | Y | Y | L | V | T | E | K | Y | S | H | F | M | K | L | F | W | N | S | R | S | R | R | F | N | R
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 |
| c1htrP_ |

### PDB 1htr chain P

Region: 89 - 115
Aligned: 27
Modelled: 27
Confidence: 46.3%
Identity: 26%
PDB header:aspartyl protease
Chain: P: PDB Molecule:progastricsin (pro segment);
PDBTitle: crystal and molecular structures of human progastricsin at 1.622 angstroms resolution

Phyre2
2 |
| c2wa1A_ |

### PDB 2wa1 chain A

Region: 82 - 162
Aligned: 81
Modelled: 81
Confidence: 38.9%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:non-structural protein 5;
PDBTitle: structure of the methyltransferase domain from modoc virus,2 a flavivirus with no known vector (nkv)

Phyre2
3 |
| d2d1ha1 |

### PDB 2d1h chain A domain 1

Region: 84 - 161
Aligned: 76
Modelled: 0
Confidence: 35.5%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: TrmB-like

Phyre2
4 |
| c1hsjA_ |

### PDB 1hsj chain A

Region: 62 - 159
Aligned: 88
Modelled: 98
Confidence: 32.3%
Identity: 14%
PDB header:transcription/sugar binding protein
Chain: A: PDB Molecule:fusion protein consisting of staphylococcus
PDBTitle: sarr mbp fusion structure

Phyre2
5 |
| d2frha1 |

### PDB 2frh chain A domain 1

Region: 61 - 159
Aligned: 88
Modelled: 99
Confidence: 31.5%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
6 |
| d2etha1 |

### PDB 2eth chain A domain 1

Region: 66 - 161
Aligned: 95
Modelled: 96
Confidence: 24.4%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
7 |
| d1stza1 |

### PDB 1stz chain A domain 1

Region: 89 - 133
Aligned: 45
Modelled: 45
Confidence: 22.7%
Identity: 27%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Heat-inducible transcription repressor HrcA, N-terminal domain

Phyre2
8 |
| d1sfxa_ |

### PDB 1sfx chain A

Region: 90 - 161
Aligned: 71
Modelled: 69
Confidence: 22.5%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: TrmB-like

Phyre2
9 |
| d1jhfa1 |

### PDB 1jhf chain A domain 1

Region: 89 - 136
Aligned: 48
Modelled: 48
Confidence: 20.8%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: LexA repressor, N-terminal DNA-binding domain

Phyre2
10 |
| c2px2B_ |

### PDB 2px2 chain B

Region: 82 - 162
Aligned: 81
Modelled: 81
Confidence: 20.5%
Identity: 15%
PDB header:transferase
Chain: B: PDB Molecule:genome polyprotein [contains: capsid protein c
PDBTitle: crystal structure of the murray valley encephalitis virus2 ns5 2'-o methyltransferase domain in complex with sah3 (monoclinic form 1)

Phyre2
11 |
| d1u61a_ |

### PDB 1u61 chain A

Region: 66 - 122
Aligned: 53
Modelled: 57
Confidence: 20.3%
Identity: 19%
Fold: RNase III domain-like
Superfamily: RNase III domain-like
Family: RNase III catalytic domain-like

Phyre2
12 |
| c3ctaA_ |

### PDB 3cta chain A

Region: 109 - 162
Aligned: 53
Modelled: 54
Confidence: 19.5%
Identity: 19%
PDB header:transferase
Chain: A: PDB Molecule:riboflavin kinase;
PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum

Phyre2
13 |
| d1lnwa_ |

### PDB 1lnw chain A

Region: 59 - 162
Aligned: 99
Modelled: 102
Confidence: 18.1%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
14 |
| c1stzB_ |

### PDB 1stz chain B

Region: 89 - 133
Aligned: 45
Modelled: 45
Confidence: 16.8%
Identity: 29%
PDB header:transcription
Chain: B: PDB Molecule:heat-inducible transcription repressor hrca homolog;
PDBTitle: crystal structure of a hypothetical protein at 2.2 a resolution

Phyre2
15 |
| c2colA_ |

### PDB 2col chain A

Region: 115 - 138
Aligned: 23
Modelled: 24
Confidence: 16.1%
Identity: 17%
PDB header:lyase/metal binding protein
Chain: A: PDB Molecule:bifunctional hemolysin-adenylate cyclase;
PDBTitle: crystal structure analysis of cyaa/c-cam with pyrophosphate

Phyre2
16 |
| d1s58a_ |

### PDB 1s58 chain A

Region: 31 - 48
Aligned: 18
Modelled: 18
Confidence: 15.7%
Identity: 33%
Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily: ssDNA viruses
Family: Parvoviridae-like VP

Phyre2
17 |
| d1ub9a_ |

### PDB 1ub9 chain A

Region: 109 - 161
Aligned: 53
Modelled: 53
Confidence: 15.6%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
18 |
| c1ykuB_ |

### PDB 1yku chain B

Region: 97 - 115
Aligned: 19
Modelled: 19
Confidence: 14.8%
Identity: 16%
PDB header:unknown function
Chain: B: PDB Molecule:hypothetical protein pxo2-61;
PDBTitle: crystal structure of a sensor domain homolog

Phyre2
19 |
| d1t3la2 |

### PDB 1t3l chain A domain 2

Region: 89 - 117
Aligned: 28
Modelled: 29
Confidence: 14.1%
Identity: 29%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Nucleotide and nucleoside kinases

Phyre2
20 |
| d1p4xa2 |

### PDB 1p4x chain A domain 2

Region: 61 - 162
Aligned: 92
Modelled: 102
Confidence: 12.7%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
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70 |
71 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1htrP_ |
|  | 46.3 | 26 | PDB header:aspartyl protease Chain: P: PDB Molecule:progastricsin (pro segment); PDBTitle: crystal and molecular structures of human progastricsin at 1.622 angstroms resolution
2 | c2wa1A_ |
|  | 38.9 | 14 | PDB header:transferase Chain: A: PDB Molecule:non-structural protein 5; PDBTitle: structure of the methyltransferase domain from modoc virus,2 a flavivirus with no known vector (nkv)
3 | d2d1ha1 |
|  | 35.5 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
4 | c1hsjA_ |
|  | 32.3 | 14 | PDB header:transcription/sugar binding protein Chain: A: PDB Molecule:fusion protein consisting of staphylococcus PDBTitle: sarr mbp fusion structure
5 | d2frha1 |
|  | 31.5 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
6 | d2etha1 |
|  | 24.4 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
7 | d1stza1 |
|  | 22.7 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
8 | d1sfxa_ |
|  | 22.5 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
9 | d1jhfa1 |
|  | 20.8 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain
10 | c2px2B_ |
|  | 20.5 | 15 | PDB header:transferase Chain: B: PDB Molecule:genome polyprotein [contains: capsid protein c PDBTitle: crystal structure of the murray valley encephalitis virus2 ns5 2'-o methyltransferase domain in complex with sah3 (monoclinic form 1)
11 | d1u61a_ |
|  | 20.3 | 19 | Fold:RNase III domain-like Superfamily:RNase III domain-like Family:RNase III catalytic domain-like
12 | c3ctaA_ |
|  | 19.5 | 19 | PDB header:transferase Chain: A: PDB Molecule:riboflavin kinase; PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
13 | d1lnwa_ |
|  | 18.1 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
14 | c1stzB_ |
|  | 16.8 | 29 | PDB header:transcription Chain: B: PDB Molecule:heat-inducible transcription repressor hrca homolog; PDBTitle: crystal structure of a hypothetical protein at 2.2 a resolution
15 | c2colA_ |
|  | 16.1 | 17 | PDB header:lyase/metal binding protein Chain: A: PDB Molecule:bifunctional hemolysin-adenylate cyclase; PDBTitle: crystal structure analysis of cyaa/c-cam with pyrophosphate
16 | d1s58a_ |
|  | 15.7 | 33 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP
17 | d1ub9a_ |
|  | 15.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
18 | c1ykuB_ |
|  | 14.8 | 16 | PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein pxo2-61; PDBTitle: crystal structure of a sensor domain homolog
19 | d1t3la2 |
|  | 14.1 | 29 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases
20 | d1p4xa2 |
|  | 12.7 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
21 | d2fbha1 |
| not modelled | 12.7 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
22 | c1z1cA_ |
| not modelled | 12.3 | 24 | PDB header:virus/dna Chain: A: PDB Molecule:coat protein vp2; PDBTitle: structural determinants of tissue tropism and in vivo2 pathogenicity for the parvovirus minute virus of mice
23 | d1nava_ |
| not modelled | 12.3 | 11 | Fold:Nuclear receptor ligand-binding domain Superfamily:Nuclear receptor ligand-binding domain Family:Nuclear receptor ligand-binding domain
24 | c3da5A_ |
| not modelled | 11.5 | 42 | PDB header:rna binding protein Chain: A: PDB Molecule:argonaute; PDBTitle: crystal structure of piwi/argonaute/zwille(paz) domain from2 thermococcus thioreducens
25 | c3h8dE_ |
| not modelled | 11.3 | 42 | PDB header:motor protein/signaling protein Chain: E: PDB Molecule:disabled homolog 2; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide
26 | c3u5gK_ |
| not modelled | 11.0 | 21 | PDB header:ribosome Chain: K: PDB Molecule:40s ribosomal protein s10-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution
27 | d1mvma_ |
| not modelled | 10.8 | 24 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP
28 | d1k3va_ |
| not modelled | 10.7 | 33 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP
29 | c1k3vA_ |
| not modelled | 10.7 | 33 | PDB header:virus Chain: A: PDB Molecule:capsid protein vp2; PDBTitle: porcine parvovirus capsid
30 | c3cjnA_ |
| not modelled | 10.5 | 15 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
31 | d2gmga1 |
| not modelled | 10.5 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF0610-like
32 | c3nttA_ |
| not modelled | 10.3 | 18 | PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: structural insights of adeno-associated virus 5. a gene therapy vector2 for cystic fibrosis
33 | d1hsja1 |
| not modelled | 10.2 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
34 | d1k8ta_ |
| not modelled | 10.0 | 13 | Fold:Adenylylcyclase toxin (the edema factor) Superfamily:Adenylylcyclase toxin (the edema factor) Family:Adenylylcyclase toxin (the edema factor)
35 | c3dkxA_ |
| not modelled | 9.9 | 18 | PDB header:replication Chain: A: PDB Molecule:replication protein repb; PDBTitle: crystal structure of the replication initiator protein2 encoded on plasmid pmv158 (repb), trigonal form, to 2.7 ang3 resolution
36 | c2xzm7_ |
| not modelled | 9.8 | 14 | PDB header:ribosome Chain: 7: PDB Molecule:plectin/s10 domain containing protein; 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
37 | d1c8da_ |
| not modelled | 9.6 | 22 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP
38 | c3kieF_ |
| not modelled | 9.6 | 12 | PDB header:virus Chain: F: PDB Molecule:capsid protein vp1; PDBTitle: crystal structure of adeno-associated virus serotype 3b
39 | d1lp3a_ |
| not modelled | 9.6 | 12 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP
40 | c2j8pA_ |
| not modelled | 9.1 | 19 | PDB header:nuclear protein Chain: A: PDB Molecule:cleavage stimulation factor 64 kda subunit; PDBTitle: nmr structure of c-terminal domain of human cstf-64
41 | c2g8gA_ |
| not modelled | 9.0 | 12 | PDB header:virus Chain: A: PDB Molecule:capsid; PDBTitle: structurally mapping the diverse phenotype of adeno-2 associated virus serotype 4
42 | c4a5mH_ |
| not modelled | 8.7 | 22 | PDB header:transcription Chain: H: PDB Molecule:uncharacterized hth-type transcriptional regulator yybr; PDBTitle: redox regulator hypr in its oxidized form
43 | c3bjaA_ |
| not modelled | 8.5 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family, putative; PDBTitle: crystal structure of putative marr-like transcription regulator2 (np_978771.1) from bacillus cereus atcc 10987 at 2.38 a resolution
44 | c2jtvA_ |
| not modelled | 7.9 | 18 | PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384
45 | c3pmdA_ |
| not modelled | 7.3 | 16 | PDB header:lipid binding protein Chain: A: PDB Molecule:conserved domain protein; PDBTitle: crystal structure of the sporulation inhibitor pxo1-118 from bacillus2 anthracis
46 | c1xfzA_ |
| not modelled | 7.2 | 13 | PDB header:lyase/metal binding protein Chain: A: PDB Molecule:calmodulin-sensitive adenylate cyclase; PDBTitle: crystal structure of anthrax edema factor (ef) in complex2 with calmodulin in the presence of 1 millimolar3 exogenously added calcium chloride
47 | c1xfuE_ |
| not modelled | 7.2 | 13 | PDB header:lyase/metal binding protein Chain: E: PDB Molecule:calmodulin-sensitive adenylate cyclase; PDBTitle: crystal structure of anthrax edema factor (ef) truncation2 mutant, ef-delta 64 in complex with calmodulin
48 | c2gslE_ |
| not modelled | 7.2 | 15 | PDB header:structural genomics, unknown function Chain: E: PDB Molecule:hypothetical protein; PDBTitle: x-ray crystal structure of protein fn1578 from fusobacterium2 nucleatum. northeast structural genomics consortium target nr1.
49 | d2i9ca1 |
| not modelled | 6.9 | 8 | Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:RPA1889-like
50 | d1bh9b_ |
| not modelled | 6.6 | 33 | Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs
51 | d2j5pa1 |
| not modelled | 6.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FtsK C-terminal domain-like
52 | c2oqgA_ |
| not modelled | 6.5 | 8 | PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
53 | d1okra_ |
| not modelled | 6.3 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Penicillinase repressor
54 | c3obhA_ |
| not modelled | 6.2 | 36 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: x-ray crystal structure of protein sp_0782 (7-79) from streptococcus2 pneumoniae. northeast structural genomics consortium target spr104
55 | d1dmga_ |
| not modelled | 6.2 | 13 | Fold:Ribosomal protein L4 Superfamily:Ribosomal protein L4 Family:Ribosomal protein L4
56 | c2qenA_ |
| not modelled | 6.2 | 14 | PDB header:unknown function Chain: A: PDB Molecule:walker-type atpase; PDBTitle: the walker-type atpase paby2304 of pyrococcus abyssi
57 | d2b50a1 |
| not modelled | 6.1 | 12 | Fold:Nuclear receptor ligand-binding domain Superfamily:Nuclear receptor ligand-binding domain Family:Nuclear receptor ligand-binding domain
58 | c3f6oB_ |
| not modelled | 6.1 | 10 | PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
59 | c2w9yA_ |
| not modelled | 5.9 | 14 | PDB header:lipid transport Chain: A: PDB Molecule:fatty acid/retinol binding protein protein 7, PDBTitle: the structure of the lipid binding protein ce-far-7 from2 caenorhabditis elegans
60 | d1y88a1 |
| not modelled | 5.9 | 23 | Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:Hypothetical protein AF1548, C-terminal domain
61 | c1fpvA_ |
| not modelled | 5.9 | 22 | PDB header:virus Chain: A: PDB Molecule:feline panleukopenia virus (strain b) viral PDBTitle: structure determination of feline panleukopenia virus empty2 particles
62 | c2b1wA_ |
| not modelled | 5.8 | 17 | PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain protein 4; PDBTitle: solution structure of the nod1 caspase activating and recruitment2 domain
63 | c3g3zA_ |
| not modelled | 5.8 | 20 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
64 | d1q3ma_ |
| not modelled | 5.8 | 44 | Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain
65 | d1q8ha_ |
| not modelled | 5.7 | 44 | Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain
66 | c1q8hA_ |
| not modelled | 5.7 | 44 | PDB header:metal binding protein Chain: A: PDB Molecule:osteocalcin; PDBTitle: crystal structure of porcine osteocalcin
67 | d2olua1 |
| not modelled | 5.7 | 16 | Fold:Lysozyme-like Superfamily:Lysozyme-like Family:PBP transglycosylase domain-like
68 | d1un2a_ |
| not modelled | 5.6 | 16 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbA-like
69 | d1pq9a_ |
| not modelled | 5.4 | 11 | Fold:Nuclear receptor ligand-binding domain Superfamily:Nuclear receptor ligand-binding domain Family:Nuclear receptor ligand-binding domain
70 | c3elkA_ |
| not modelled | 5.3 | 15 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcriptional regulator ta0346; PDBTitle: crystal structure of putative transcriptional regulator ta0346 from2 thermoplasma acidophilum
71 | c2nyxB_ |
| not modelled | 5.3 | 10 | PDB header:transcription Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404; PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis

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