Phyre 2 Results for P32711

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Email | l.a.kelley@imperial.ac.uk
Description | P32711
Date | Thu Jan 5 11:50:30 GMT 2012
Unique Job ID | d3229b40593ee259

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2hl7A_
Top template information
PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa
Confidence and coverage
Confidence: | 100.0% | Coverage: | 65%
82 residues ( 65% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | V | S | M | R | H | Q | V | Y | S | M | V | A | E | G | K | N | E | V | E | I | I | G | W | M | T | E | R | Y | G | D | F | V | R | Y | N | P | P | L | T | G | Q | T | L | V | L | W | A | L | P | V | V | L | L | L | L | M | A | L | I | L
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Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | .
Sequence |  | W | R | V | R | A | K | 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 |
| c2hl7A_ |

### PDB 2hl7 chain A

Region: 16 - 97
Aligned: 82
Modelled: 82
Confidence: 100.0%
Identity: 44%
PDB header:oxidoreductase
Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh;
PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa

Phyre2
2 |
| c2kw0A_ |

### PDB 2kw0 chain A

Region: 20 - 100
Aligned: 81
Modelled: 81
Confidence: 100.0%
Identity: 43%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ccmh protein;
PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli

Phyre2
3 |
| d1pbya1 |

### PDB 1pby chain A domain 1

Region: 43 - 105
Aligned: 60
Modelled: 63
Confidence: 73.5%
Identity: 15%
Fold: Cytochrome c
Superfamily: Cytochrome c
Family: Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2

Phyre2
4 |
| c2qsrA_ |

### PDB 2qsr chain A

Region: 61 - 90
Aligned: 30
Modelled: 30
Confidence: 66.4%
Identity: 17%
PDB header:transcription
Chain: A: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of c-terminal domain of transcription-repair2 coupling factor

Phyre2
5 |
| d2eyqa6 |

### PDB 2eyq chain A domain 6

Region: 61 - 90
Aligned: 30
Modelled: 30
Confidence: 62.8%
Identity: 37%
Fold: TRCF domain-like
Superfamily: TRCF domain-like
Family: TRCF domain

Phyre2
6 |
| c3omdB_ |

### PDB 3omd chain B

Region: 65 - 86
Aligned: 22
Modelled: 22
Confidence: 62.2%
Identity: 9%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of unknown function protein from leptospirillum2 rubarum

Phyre2
7 |
| c2c4rL_ |

### PDB 2c4r chain L

Region: 44 - 92
Aligned: 49
Modelled: 49
Confidence: 61.0%
Identity: 18%
PDB header:hydrolase
Chain: L: PDB Molecule:ribonuclease e;
PDBTitle: catalytic domain of e. coli rnase e

Phyre2
8 |
| d1r5ya_ |

### PDB 1r5y chain A

Region: 44 - 88
Aligned: 45
Modelled: 45
Confidence: 59.8%
Identity: 16%
Fold: TIM beta/alpha-barrel
Superfamily: tRNA-guanine transglycosylase
Family: tRNA-guanine transglycosylase

Phyre2
9 |
| c2x48B_ |

### PDB 2x48 chain B

Region: 62 - 84
Aligned: 23
Modelled: 23
Confidence: 54.4%
Identity: 9%
PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1

Phyre2
10 |
| c2bpbB_ |

### PDB 2bpb chain B

Region: 43 - 88
Aligned: 46
Modelled: 46
Confidence: 54.1%
Identity: 17%
PDB header:oxidoreductase
Chain: B: PDB Molecule:sulfite\:cytochrome c oxidoreductase subunit b;
PDBTitle: sulfite dehydrogenase from starkeya novella

Phyre2
11 |
| c3lm3A_ |

### PDB 3lm3 chain A

Region: 68 - 104
Aligned: 37
Modelled: 34
Confidence: 52.1%
Identity: 27%
PDB header:unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a putative glycoside hydrolase/deacetylase2 (bdi_3119) from parabacteroides distasonis at 1.44 a resolution

Phyre2
12 |
| d1jmxa1 |

### PDB 1jmx chain A domain 1

Region: 43 - 89
Aligned: 47
Modelled: 47
Confidence: 46.9%
Identity: 13%
Fold: Cytochrome c
Superfamily: Cytochrome c
Family: Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2

Phyre2
13 |
| c3d3mB_ |

### PDB 3d3m chain B

Region: 61 - 96
Aligned: 36
Modelled: 36
Confidence: 46.4%
Identity: 6%
PDB header:translation
Chain: B: PDB Molecule:eukaryotic translation initiation factor 4 gamma
PDBTitle: the crystal structure of the c-terminal region of death2 associated protein 5(dap5)

Phyre2
14 |
| d1fs1b1 |

### PDB 1fs1 chain B domain 1

Region: 65 - 84
Aligned: 19
Modelled: 20
Confidence: 42.6%
Identity: 32%
Fold: Skp1 dimerisation domain-like
Superfamily: Skp1 dimerisation domain-like
Family: Skp1 dimerisation domain-like

Phyre2
15 |
| d1fs2b1 |

### PDB 1fs2 chain B domain 1

Region: 65 - 84
Aligned: 19
Modelled: 20
Confidence: 40.6%
Identity: 32%
Fold: Skp1 dimerisation domain-like
Superfamily: Skp1 dimerisation domain-like
Family: Skp1 dimerisation domain-like

Phyre2
16 |
| d1ug3a2 |

### PDB 1ug3 chain A domain 2

Region: 61 - 96
Aligned: 36
Modelled: 36
Confidence: 39.1%
Identity: 11%
Fold: alpha-alpha superhelix
Superfamily: ARM repeat
Family: MIF4G domain-like

Phyre2
17 |
| c1iq8B_ |

### PDB 1iq8 chain B

Region: 44 - 75
Aligned: 32
Modelled: 32
Confidence: 38.6%
Identity: 38%
PDB header:transferase
Chain: B: PDB Molecule:archaeosine trna-guanine transglycosylase;
PDBTitle: crystal structure of archaeosine trna-guanine2 transglycosylase from pyrococcus horikoshii

Phyre2
18 |
| d1iq8a1 |

### PDB 1iq8 chain A domain 1

Region: 44 - 87
Aligned: 44
Modelled: 44
Confidence: 38.2%
Identity: 20%
Fold: TIM beta/alpha-barrel
Superfamily: tRNA-guanine transglycosylase
Family: tRNA-guanine transglycosylase

Phyre2
19 |
| d1jm7a_ |

### PDB 1jm7 chain A

Region: 21 - 49
Aligned: 29
Modelled: 29
Confidence: 37.1%
Identity: 21%
Fold: RING/U-box
Superfamily: RING/U-box
Family: RING finger domain, C3HC4

Phyre2
20 |
| d1nexa1 |

### PDB 1nex chain A domain 1

Region: 65 - 84
Aligned: 19
Modelled: 20
Confidence: 35.8%
Identity: 21%
Fold: Skp1 dimerisation domain-like
Superfamily: Skp1 dimerisation domain-like
Family: Skp1 dimerisation domain-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2hl7A_ |
|  | 100.0 | 44 | PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa
2 | c2kw0A_ |
|  | 100.0 | 43 | PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli
3 | d1pbya1 |
|  | 73.5 | 15 | Fold:Cytochrome c Superfamily:Cytochrome c Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
4 | c2qsrA_ |
|  | 66.4 | 17 | PDB header:transcription Chain: A: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of c-terminal domain of transcription-repair2 coupling factor
5 | d2eyqa6 |
|  | 62.8 | 37 | Fold:TRCF domain-like Superfamily:TRCF domain-like Family:TRCF domain
6 | c3omdB_ |
|  | 62.2 | 9 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of unknown function protein from leptospirillum2 rubarum
7 | c2c4rL_ |
|  | 61.0 | 18 | PDB header:hydrolase Chain: L: PDB Molecule:ribonuclease e; PDBTitle: catalytic domain of e. coli rnase e
8 | d1r5ya_ |
|  | 59.8 | 16 | Fold:TIM beta/alpha-barrel Superfamily:tRNA-guanine transglycosylase Family:tRNA-guanine transglycosylase
9 | c2x48B_ |
|  | 54.4 | 9 | PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
10 | c2bpbB_ |
|  | 54.1 | 17 | PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite\:cytochrome c oxidoreductase subunit b; PDBTitle: sulfite dehydrogenase from starkeya novella
11 | c3lm3A_ |
|  | 52.1 | 27 | PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative glycoside hydrolase/deacetylase2 (bdi_3119) from parabacteroides distasonis at 1.44 a resolution
12 | d1jmxa1 |
|  | 46.9 | 13 | Fold:Cytochrome c Superfamily:Cytochrome c Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
13 | c3d3mB_ |
|  | 46.4 | 6 | PDB header:translation Chain: B: PDB Molecule:eukaryotic translation initiation factor 4 gamma PDBTitle: the crystal structure of the c-terminal region of death2 associated protein 5(dap5)
14 | d1fs1b1 |
|  | 42.6 | 32 | Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like
15 | d1fs2b1 |
|  | 40.6 | 32 | Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like
16 | d1ug3a2 |
|  | 39.1 | 11 | Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:MIF4G domain-like
17 | c1iq8B_ |
|  | 38.6 | 38 | PDB header:transferase Chain: B: PDB Molecule:archaeosine trna-guanine transglycosylase; PDBTitle: crystal structure of archaeosine trna-guanine2 transglycosylase from pyrococcus horikoshii
18 | d1iq8a1 |
|  | 38.2 | 20 | Fold:TIM beta/alpha-barrel Superfamily:tRNA-guanine transglycosylase Family:tRNA-guanine transglycosylase
19 | d1jm7a_ |
|  | 37.1 | 21 | Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4
20 | d1nexa1 |
|  | 35.8 | 21 | Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like
21 | c2ashB_ |
| not modelled | 35.5 | 25 | PDB header:transferase Chain: B: PDB Molecule:queuine trna-ribosyltransferase; PDBTitle: crystal structure of queuine trna-ribosyltransferase (ec 2.4.2.29)2 (trna-guanine (tm1561) from thermotoga maritima at 1.90 a resolution
22 | d1ef4a_ |
| not modelled | 35.4 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:RNA polymerase subunit RPB10 Family:RNA polymerase subunit RPB10
23 | c2jq5A_ |
| not modelled | 35.1 | 14 | PDB header:structural genomics Chain: A: PDB Molecule:sec-c motif; PDBTitle: solution structure of rpa3114, a sec-c motif containing2 protein from rhodopseudomonas palustris; northeast3 structural genomics consortium target rpt5 / ontario4 center for structural proteomics target rp3097
24 | d6paxa1 |
| not modelled | 33.7 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
25 | c2eyqA_ |
| not modelled | 32.9 | 33 | PDB header:hydrolase Chain: A: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor
26 | c1u78A_ |
| not modelled | 30.8 | 14 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
27 | c3floD_ |
| not modelled | 29.1 | 21 | PDB header:transferase Chain: D: PDB Molecule:dna polymerase alpha catalytic subunit a; PDBTitle: crystal structure of the carboxyl-terminal domain of yeast2 dna polymerase alpha in complex with its b subunit
28 | d2gmga1 |
| not modelled | 28.6 | 42 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF0610-like
29 | d1wgna_ |
| not modelled | 27.0 | 22 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain
30 | c2opfA_ |
| not modelled | 26.3 | 67 | PDB header:hydrolase/dna Chain: A: PDB Molecule:endonuclease viii; PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
31 | c3b40A_ |
| not modelled | 25.1 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:probable dipeptidase; PDBTitle: crystal structure of the probable dipeptidase pvdm from2 pseudomonas aeruginosa
32 | d1k78a1 |
| not modelled | 24.4 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
33 | d1p7ia_ |
| not modelled | 23.9 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
34 | c3hosA_ |
| not modelled | 23.3 | 21 | PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
35 | c2qeuA_ |
| not modelled | 22.7 | 8 | PDB header:lyase Chain: A: PDB Molecule:putative carboxymuconolactone decarboxylase; PDBTitle: crystal structure of putative carboxymuconolactone decarboxylase2 (yp_555818.1) from burkholderia xenovorans lb400 at 1.65 a resolution
36 | c3llkA_ |
| not modelled | 22.7 | 28 | PDB header:oxidoreductase Chain: A: PDB Molecule:sulfhydryl oxidase 1; PDBTitle: sulfhydryl oxidase fragment of human qsox1
37 | c3iz6X_ |
| not modelled | 22.7 | 24 | PDB header:ribosome Chain: X: PDB Molecule:40s ribosomal protein s27 (s27e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
38 | c3g2bA_ |
| not modelled | 21.9 | 8 | PDB header:biosynthetic protein Chain: A: PDB Molecule:coenzyme pqq synthesis protein d; PDBTitle: crystal structure of pqqd from xanthomonas campestris
39 | d1od6a_ |
| not modelled | 21.0 | 12 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
40 | d2ovra1 |
| not modelled | 20.9 | 32 | Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like
41 | d1qxfa_ |
| not modelled | 20.5 | 18 | Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein S27e
42 | c2ragB_ |
| not modelled | 20.0 | 16 | PDB header:hydrolase Chain: B: PDB Molecule:dipeptidase; PDBTitle: crystal structure of aminohydrolase from caulobacter crescentus
43 | c3b9bA_ |
| not modelled | 20.0 | 12 | PDB header:hydrolase Chain: A: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: structure of the e2 beryllium fluoride complex of the serca2 ca2+-atpase
44 | d1eb7a2 |
| not modelled | 20.0 | 22 | Fold:Cytochrome c Superfamily:Cytochrome c Family:Di-heme cytochrome c peroxidase
45 | c1ug3A_ |
| not modelled | 19.8 | 13 | PDB header:translation Chain: A: PDB Molecule:eukaryotic protein synthesis initiation factor PDBTitle: c-terminal portion of human eif4gi
46 | c2jnhA_ |
| not modelled | 19.7 | 13 | PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of the uba domain from cbl-b
47 | d1p91a_ |
| not modelled | 19.4 | 31 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:rRNA methyltransferase RlmA
48 | d1odfa_ |
| not modelled | 19.3 | 26 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Phosphoribulokinase/pantothenate kinase
49 | d2ga1a1 |
| not modelled | 18.9 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Alr1493-like
50 | c1nexC_ |
| not modelled | 18.7 | 21 | PDB header:ligase, cell cycle Chain: C: PDB Molecule:centromere dna-binding protein complex cbf3 PDBTitle: crystal structure of scskp1-sccdc4-cpd peptide complex
51 | c1ztbA_ |
| not modelled | 18.7 | 15 | PDB header:ligase Chain: A: PDB Molecule:chorismate synthase; PDBTitle: crystal structure of chorismate synthase from mycobacterium2 tuberculosis
52 | c3o0rC_ |
| not modelled | 18.6 | 13 | PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment
53 | c2pmzN_ |
| not modelled | 18.2 | 18 | PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
54 | c2jr6A_ |
| not modelled | 18.0 | 33 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0434 protein nma0874; PDBTitle: solution structure of upf0434 protein nma0874. northeast structural2 genomics target mr32
55 | c3lrqB_ |
| not modelled | 18.0 | 30 | PDB header:ligase Chain: B: PDB Molecule:e3 ubiquitin-protein ligase trim37; PDBTitle: crystal structure of the u-box domain of human ubiquitin-2 protein ligase (e3), northeast structural genomics3 consortium target hr4604d.
56 | c2js4A_ |
| not modelled | 17.9 | 44 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0434 protein bb2007; PDBTitle: solution nmr structure of bordetella bronchiseptica protein2 bb2007. northeast structural genomics consortium target3 bor54
57 | c2jvwA_ |
| not modelled | 17.4 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of uncharacterized protein q5e7h1 from vibrio2 fischeri. northeast structural genomics target vfr117
58 | c2xzmO_ |
| not modelled | 17.2 | 10 | PDB header:ribosome Chain: O: PDB Molecule:rps13e; 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
59 | d1y0ua_ |
| not modelled | 17.1 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
60 | d2cwqa1 |
| not modelled | 17.0 | 13 | Fold:AhpD-like Superfamily:AhpD-like Family:TTHA0727-like
61 | c3axjB_ |
| not modelled | 16.9 | 7 | PDB header:dna binding protein Chain: B: PDB Molecule:translin associated factor x, isoform b; PDBTitle: high resolution crystal structure of c3po
62 | c2p1nD_ |
| not modelled | 16.3 | 32 | PDB header:signaling protein Chain: D: PDB Molecule:skp1-like protein 1a; PDBTitle: mechanism of auxin perception by the tir1 ubiqutin ligase
63 | d1lv3a_ |
| not modelled | 16.1 | 22 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Hypothetical zinc finger protein YacG
64 | c2ecgA_ |
| not modelled | 16.0 | 9 | PDB header:apoptosis Chain: A: PDB Molecule:baculoviral iap repeat-containing protein 4; PDBTitle: solution structure of the ring domain of the baculoviral2 iap repeat-containing protein 4 from homo sapiens
65 | d2lfba_ |
| not modelled | 16.0 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
66 | d1sxjd1 |
| not modelled | 15.3 | 14 | Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain
67 | c3itcA_ |
| not modelled | 15.2 | 4 | PDB header:hydrolase Chain: A: PDB Molecule:renal dipeptidase; PDBTitle: crystal structure of sco3058 with bound citrate and glycerol
68 | d2gmya1 |
| not modelled | 15.2 | 14 | Fold:AhpD-like Superfamily:AhpD-like Family:Atu0492-like
69 | d2c0sa1 |
| not modelled | 14.9 | 43 | Fold:ROP-like Superfamily:BAS1536-like Family:BAS1536-like
70 | c3s93B_ |
| not modelled | 14.5 | 12 | PDB header:transcription Chain: B: PDB Molecule:tudor domain-containing protein 5; PDBTitle: crystal structure of conserved motif in tdrd5
71 | d1itua_ |
| not modelled | 14.5 | 12 | Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:Renal dipeptidase
72 | c3a44D_ |
| not modelled | 14.5 | 36 | PDB header:metal binding protein Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa; PDBTitle: crystal structure of hypa in the dimeric form
73 | c2d9sA_ |
| not modelled | 14.4 | 10 | PDB header:ligase Chain: A: PDB Molecule:cbl e3 ubiquitin protein ligase; PDBTitle: solution structure of rsgi ruh-049, a uba domain from mouse2 cdna
74 | d1dl6a_ |
| not modelled | 14.4 | 25 | Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain
75 | c3izbX_ |
| not modelled | 14.3 | 33 | PDB header:ribosome Chain: X: PDB Molecule:40s ribosomal protein rps27 (s27e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
76 | c3lpeF_ |
| not modelled | 14.3 | 24 | PDB header:transferase Chain: F: PDB Molecule:dna-directed rna polymerase subunit e''; PDBTitle: crystal structure of spt4/5ngn heterodimer complex from methanococcus2 jannaschii
77 | c1b6aA_ |
| not modelled | 14.3 | 21 | PDB header:angiogenesis inhibitor Chain: A: PDB Molecule:methionine aminopeptidase; PDBTitle: human methionine aminopeptidase 2 complexed with tnp-470
78 | d2c2vv1 |
| not modelled | 14.2 | 13 | Fold:RING/U-box Superfamily:RING/U-box Family:U-box
79 | c3pjaK_ |
| not modelled | 13.9 | 13 | PDB header:hydrolase Chain: K: PDB Molecule:translin-associated protein x; PDBTitle: crystal structure of human c3po complex
80 | d2cqxa1 |
| not modelled | 13.8 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
81 | c3qw4B_ |
| not modelled | 13.8 | 15 | PDB header:transferase, lyase Chain: B: PDB Molecule:ump synthase; PDBTitle: structure of leishmania donovani ump synthase
82 | c1dl0A_ |
| not modelled | 13.7 | 46 | PDB header:toxin Chain: A: PDB Molecule:j-atracotoxin-hv1c; PDBTitle: solution structure of the insecticidal neurotoxin j-2 atracotoxin-hv1c
83 | d1dl0a_ |
| not modelled | 13.7 | 46 | Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins
84 | d2jnya1 |
| not modelled | 13.6 | 33 | Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like
85 | c2xzm6_ |
| not modelled | 13.4 | 47 | PDB header:ribosome Chain: 6: PDB Molecule:rps27e; 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
86 | c1nl0G_ |
| not modelled | 13.3 | 50 | PDB header:immune system Chain: G: PDB Molecule:factor ix; PDBTitle: crystal structure of human factor ix gla domain in complex2 of an inhibitory antibody, 10c12
87 | d1jgga_ |
| not modelled | 13.1 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
88 | c3l6aA_ |
| not modelled | 13.0 | 5 | PDB header:translation Chain: A: PDB Molecule:eukaryotic translation initiation factor 4 gamma 2; PDBTitle: crystal structure of the c-terminal region of human p97
89 | d1o6ba_ |
| not modelled | 12.9 | 8 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
90 | c3fdgA_ |
| not modelled | 12.6 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:dipeptidase ac. metallo peptidase. merops family m19; PDBTitle: the crystal structure of the dipeptidase ac, metallo peptidase. merops2 family m19
91 | d1xkpa1 |
| not modelled | 12.3 | 14 | Fold:Type III secretion system domain Superfamily:Type III secretion system domain Family:LcrE-like
92 | c2ao9H_ |
| not modelled | 12.2 | 13 | PDB header:structural genomics, unknown function Chain: H: PDB Molecule:phage protein; PDBTitle: structural genomics, the crystal structure of a phage protein2 (phbc6a51) from bacillus cereus atcc 14579
93 | c2kpiA_ |
| not modelled | 12.1 | 44 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sco3027; PDBTitle: solution nmr structure of streptomyces coelicolor sco30272 modeled with zn+2 bound, northeast structural genomics3 consortium target rr58
94 | d2ao9a1 |
| not modelled | 12.0 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Nanomeric phage protein-like
95 | c1ee8A_ |
| not modelled | 11.9 | 57 | PDB header:dna binding protein Chain: A: PDB Molecule:mutm (fpg) protein; PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
96 | d1d8ja_ |
| not modelled | 11.9 | 33 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:The central core domain of TFIIE beta
97 | c3bg3B_ |
| not modelled | 11.9 | 10 | PDB header:ligase Chain: B: PDB Molecule:pyruvate carboxylase, mitochondrial; PDBTitle: crystal structure of human pyruvate carboxylase (missing2 the biotin carboxylase domain at the n-terminus)
98 | c2do6A_ |
| not modelled | 11.9 | 15 | PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of rsgi ruh-065, a uba domain from human2 cdna
99 | d1vnda_ |
| not modelled | 11.8 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain

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