Secondary structure and disorder prediction

1

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10

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20

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30

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40

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50

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60

Sequence

M

K

K

M

Q

S

I

V

L

A

L

S

L

V

L

V

A

P

M

A

A

Q

A

A

E

I

T

L

V

P

S

V

K

L

Q

I

G

D

R

D

N

R

G

Y

Y

W

D

G

G

H

W

R

D

H

G

W

W

K

Q

H

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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80

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90

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Sequence

Y

E

W

R

G

N

R

W

H

L

H

G

P

P

P

P

P

R

H

H

K

K

A

P

H

D

H

H

G

G

H

G

P

G

K

H

H

R

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

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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

PDB 3nc7 chain A Region: 52 - 96 Aligned: 45 Modelled: 45 Confidence: 20.7% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome p450 cypx; PDBTitle: cyp134a1 2-phenylimidazole bound structure Phyre2 PDB 1wj2 chain A Region: 47 - 52 Aligned: 6 Modelled: 6 Confidence: 13.8% Identity: 67% Fold: WRKY DNA-binding domain Superfamily: WRKY DNA-binding domain Family: WRKY DNA-binding domain Phyre2 PDB 2ve3 chain A Region: 52 - 96 Aligned: 45 Modelled: 45 Confidence: 10.3% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:putative cytochrome p450 120; PDBTitle: retinoic acid bound cyanobacterial cyp120a1 Phyre2 PDB 2rnm chain C Region: 22 - 47 Aligned: 26 Modelled: 26 Confidence: 10.3% Identity: 15% PDB header:protein fibril Chain: C: PDB Molecule:small s protein; PDBTitle: structure of the het-s(218-289) prion in its amyloid form2 obtained by solid-state nmr Phyre2 PDB 2ayd chain A Region: 47 - 52 Aligned: 6 Modelled: 6 Confidence: 10.0% Identity: 67% PDB header:transcription Chain: A: PDB Molecule:wrky transcription factor 1; PDBTitle: crystal structure of the c-terminal wrky domainof atwrky1,2 an sa-induced and partially npr1-dependent transcription3 factor Phyre2 PDB 1m5h chain A domain 1 Region: 1 - 52 Aligned: 51 Modelled: 52 Confidence: 9.7% Identity: 18% Fold: Ferredoxin-like Superfamily: Formylmethanofuran:tetrahydromethanopterin formyltransferase Family: Formylmethanofuran:tetrahydromethanopterin formyltransferase Phyre2 PDB 3czh chain A domain 1 Region: 52 - 96 Aligned: 44 Modelled: 45 Confidence: 9.5% Identity: 16% Fold: Cytochrome P450 Superfamily: Cytochrome P450 Family: Cytochrome P450 Phyre2 PDB 2de0 chain X Region: 22 - 49 Aligned: 23 Modelled: 28 Confidence: 9.2% Identity: 39% PDB header:transferase Chain: X: PDB Molecule:alpha-(1,6)-fucosyltransferase; PDBTitle: crystal structure of human alpha 1,6-fucosyltransferase, fut8 Phyre2 PDB 1qb5 chain D Region: 3 - 29 Aligned: 26 Modelled: 27 Confidence: 9.1% Identity: 27% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Bacterial AB5 toxins, B-subunits Phyre2 PDB 3iyu chain Y Region: 1 - 37 Aligned: 37 Modelled: 37 Confidence: 8.8% Identity: 24% PDB header:virus Chain: Y: PDB Molecule:outer capsid protein vp4; PDBTitle: atomic model of an infectious rotavirus particle Phyre2 PDB 3g1q chain C Region: 52 - 96 Aligned: 38 Modelled: 45 Confidence: 8.4% Identity: 11% PDB header:oxidoreductase Chain: C: PDB Molecule:sterol 14-alpha-demethylase; PDBTitle: crystal structure of sterol 14-alpha demethylase (cyp51)2 from trypanosoma brucei in ligand free state Phyre2 PDB 2fhj chain D Region: 1 - 53 Aligned: 52 Modelled: 53 Confidence: 8.4% Identity: 13% PDB header:transferase Chain: D: PDB Molecule:formylmethanofuran--tetrahydromethanopterin PDBTitle: crystal structure of formylmethanofuran:2 tetrahydromethanopterin formyltransferase in complex with3 its coenzymes Phyre2 PDB 1tqn chain A Region: 52 - 96 Aligned: 44 Modelled: 45 Confidence: 8.1% Identity: 14% Fold: Cytochrome P450 Superfamily: Cytochrome P450 Family: Cytochrome P450 Phyre2 PDB 1po5 chain A Region: 52 - 96 Aligned: 44 Modelled: 45 Confidence: 7.1% Identity: 9% Fold: Cytochrome P450 Superfamily: Cytochrome P450 Family: Cytochrome P450 Phyre2 PDB 3k9v chain B Region: 52 - 96 Aligned: 43 Modelled: 45 Confidence: 6.8% Identity: 12% PDB header:oxidoreductase Chain: B: PDB Molecule:1,25-dihydroxyvitamin d(3) 24-hydroxylase, PDBTitle: crystal structure of rat mitochondrial p450 24a1 s57d in2 complex with chaps Phyre2 PDB 3p5n chain A Region: 2 - 38 Aligned: 36 Modelled: 37 Confidence: 6.8% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter Phyre2 PDB 2c0z chain A Region: 16 - 50 Aligned: 35 Modelled: 35 Confidence: 6.8% Identity: 26% PDB header:isomerase Chain: A: PDB Molecule:novw; PDBTitle: the 1.6 a resolution crystal structure of novw: a 4-keto-6-2 deoxy sugar epimerase from the novobiocin biosynthetic3 gene cluster of streptomyces spheroides Phyre2 PDB 3na0 chain B Region: 52 - 96 Aligned: 43 Modelled: 45 Confidence: 6.8% Identity: 9% PDB header:oxidoreductase, electron transport Chain: B: PDB Molecule:cholesterol side-chain cleavage enzyme, mitochondrial; PDBTitle: crystal structure of human cyp11a1 in complex with 20,22-2 dihydroxycholesterol Phyre2 PDB 1nr6 chain A Region: 52 - 96 Aligned: 44 Modelled: 45 Confidence: 6.5% Identity: 7% Fold: Cytochrome P450 Superfamily: Cytochrome P450 Family: Cytochrome P450 Phyre2 PDB 2nnj chain A domain 1 Region: 52 - 96 Aligned: 44 Modelled: 45 Confidence: 5.9% Identity: 7% Fold: Cytochrome P450 Superfamily: Cytochrome P450 Family: Cytochrome P450 Phyre2 1 c3nc7A_ 2 d1wj2a_ 3 c2ve3A_ 4 c2rnmC_ 5 c2aydA_ 6 d1m5ha1 7 d3czha1 8 c2de0X_ 9 d1qb5d_ 10 c3iyuY_ 11 c3g1qC_ 12 c2fhjD_ 13 d1tqna_ 14 d1po5a_ 15 c3k9vB_ 16 c3p5nA_ 17 c2c0zA_ 18 c3na0B_ 19 d1nr6a_ 20 d2nnja1 21 22 23 24 25 26 27 28

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c3nc7A_ 20.7 13 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome p450 cypx; PDBTitle: cyp134a1 2-phenylimidazole bound structure 2 d1wj2a_ 13.8 67 Fold:WRKY DNA-binding domain Superfamily:WRKY DNA-binding domain Family:WRKY DNA-binding domain 3 c2ve3A_ 10.3 13 PDB header:oxidoreductase Chain: A: PDB Molecule:putative cytochrome p450 120; PDBTitle: retinoic acid bound cyanobacterial cyp120a1 4 c2rnmC_ 10.3 15 PDB header:protein fibril Chain: C: PDB Molecule:small s protein; PDBTitle: structure of the het-s(218-289) prion in its amyloid form2 obtained by solid-state nmr 5 c2aydA_ 10.0 67 PDB header:transcription Chain: A: PDB Molecule:wrky transcription factor 1; PDBTitle: crystal structure of the c-terminal wrky domainof atwrky1,2 an sa-induced and partially npr1-dependent transcription3 factor 6 d1m5ha1 9.7 18 Fold:Ferredoxin-like Superfamily:Formylmethanofuran:tetrahydromethanopterin formyltransferase Family:Formylmethanofuran:tetrahydromethanopterin formyltransferase 7 d3czha1 9.5 16 Fold:Cytochrome P450 Superfamily:Cytochrome P450 Family:Cytochrome P450 8 c2de0X_ 9.2 39 PDB header:transferase Chain: X: PDB Molecule:alpha-(1,6)-fucosyltransferase; PDBTitle: crystal structure of human alpha 1,6-fucosyltransferase, fut8 9 d1qb5d_ 9.1 27 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits 10 c3iyuY_ 8.8 24 PDB header:virus Chain: Y: PDB Molecule:outer capsid protein vp4; PDBTitle: atomic model of an infectious rotavirus particle 11 c3g1qC_ 8.4 11 PDB header:oxidoreductase Chain: C: PDB Molecule:sterol 14-alpha-demethylase; PDBTitle: crystal structure of sterol 14-alpha demethylase (cyp51)2 from trypanosoma brucei in ligand free state 12 c2fhjD_ 8.4 13 PDB header:transferase Chain: D: PDB Molecule:formylmethanofuran--tetrahydromethanopterin PDBTitle: crystal structure of formylmethanofuran:2 tetrahydromethanopterin formyltransferase in complex with3 its coenzymes 13 d1tqna_ 8.1 14 Fold:Cytochrome P450 Superfamily:Cytochrome P450 Family:Cytochrome P450 14 d1po5a_ 7.1 9 Fold:Cytochrome P450 Superfamily:Cytochrome P450 Family:Cytochrome P450 15 c3k9vB_ 6.8 12 PDB header:oxidoreductase Chain: B: PDB Molecule:1,25-dihydroxyvitamin d(3) 24-hydroxylase, PDBTitle: crystal structure of rat mitochondrial p450 24a1 s57d in2 complex with chaps 16 c3p5nA_ 6.8 14 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 17 c2c0zA_ 6.8 26 PDB header:isomerase Chain: A: PDB Molecule:novw; PDBTitle: the 1.6 a resolution crystal structure of novw: a 4-keto-6-2 deoxy sugar epimerase from the novobiocin biosynthetic3 gene cluster of streptomyces spheroides 18 c3na0B_ 6.8 9 PDB header:oxidoreductase, electron transport Chain: B: PDB Molecule:cholesterol side-chain cleavage enzyme, mitochondrial; PDBTitle: crystal structure of human cyp11a1 in complex with 20,22-2 dihydroxycholesterol 19 d1nr6a_ 6.5 7 Fold:Cytochrome P450 Superfamily:Cytochrome P450 Family:Cytochrome P450 20 d2nnja1 5.9 7 Fold:Cytochrome P450 Superfamily:Cytochrome P450 Family:Cytochrome P450 21 d1bvp12 not modelled 5.7 26 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 22 c3m3wA_ not modelled 5.6 25 PDB header:endocytosis Chain: A: PDB Molecule:protein kinase c and casein kinase ii substrate protein 3; PDBTitle: crystal strcuture of mouse pacsin3 bar domain mutant 23 c1yewF_ not modelled 5.4 38 PDB header:oxidoreductase, membrane protein Chain: F: PDB Molecule:particulate methane monooxygenase, a subunit; PDBTitle: crystal structure of particulate methane monooxygenase 24 d1m5sa1 not modelled 5.2 13 Fold:Ferredoxin-like Superfamily:Formylmethanofuran:tetrahydromethanopterin formyltransferase Family:Formylmethanofuran:tetrahydromethanopterin formyltransferase 25 d1h3ga1 not modelled 5.2 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes 26 c3e4eA_ not modelled 5.1 7 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome p450 2e1; PDBTitle: human cytochrome p450 2e1 in complex with the inhibitor 4-2 methylpyrazole 27 c1g92A_ not modelled 5.1 35 PDB header:toxin Chain: A: PDB Molecule:poneratoxin; PDBTitle: solution structure of poneratoxin 28 c3o0rC_ not modelled 5.0 15 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

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

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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 Disclaimer Terms and Conditions	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