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

S

R

A

L

F

A

V

V

L

A

F

P

L

I

A

L

A

N

P

H

Y

R

P

D

V

E

V

N

V

P

P

E

V

F

S

S

G

G

Q

S

A

Q

P

C

T

Q

C

C

V

Y

Q

D

Q

N

Y

S

E

G

A

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

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90

Sequence

V

I

K

A

E

G

I

L

L

Q

C

Q

R

D

D

K

T

L

S

T

N

P

L

V

W

R

R

V

K

P

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 2wy3 chain B Region: 29 - 53 Aligned: 21 Modelled: 25 Confidence: 29.3% Identity: 29% PDB header:immune system/viral protein Chain: B: PDB Molecule:uncharacterized protein ul16; PDBTitle: structure of the hcmv ul16-micb complex elucidates select2 binding of a viral immunoevasin to diverse nkg2d ligands Phyre2 PDB 2o01 chain I Region: 2 - 18 Aligned: 17 Modelled: 17 Confidence: 29.2% Identity: 41% PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2rkz chain D Region: 49 - 72 Aligned: 24 Modelled: 24 Confidence: 27.8% Identity: 25% PDB header:cell adhesion Chain: D: PDB Molecule:fibronectin; PDBTitle: crystal structure of the second and third fibronectin f12 modules in complex with a fragment of staphylococcus3 aureus fnbpa-1 Phyre2 PDB 1zue chain A domain 1 Region: 43 - 51 Aligned: 9 Modelled: 9 Confidence: 25.6% Identity: 33% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 PDB 1nps chain A Region: 47 - 68 Aligned: 22 Modelled: 22 Confidence: 21.1% Identity: 14% Fold: gamma-Crystallin-like Superfamily: gamma-Crystallin-like Family: Crystallins/Ca-binding development proteins Phyre2 PDB 1wv3 chain A domain 2 Region: 53 - 74 Aligned: 21 Modelled: 22 Confidence: 19.4% Identity: 43% Fold: SMAD/FHA domain Superfamily: SMAD/FHA domain Family: EssC N-terminal domain-like Phyre2 PDB 2fok chain A domain 4 Region: 50 - 59 Aligned: 10 Modelled: 10 Confidence: 17.7% Identity: 30% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Restriction endonuclease FokI, C-terminal (catalytic) domain Phyre2 PDB 1u5m chain A Region: 49 - 66 Aligned: 18 Modelled: 18 Confidence: 16.5% Identity: 39% Fold: FnI-like domain Superfamily: FnI-like domain Family: VWC domain Phyre2 PDB 1prs chain A domain 2 Region: 47 - 68 Aligned: 22 Modelled: 22 Confidence: 14.5% Identity: 9% Fold: gamma-Crystallin-like Superfamily: gamma-Crystallin-like Family: Crystallins/Ca-binding development proteins Phyre2 PDB 3lw5 chain I Region: 2 - 18 Aligned: 17 Modelled: 17 Confidence: 13.8% Identity: 41% PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2wse chain I Region: 2 - 18 Aligned: 17 Modelled: 17 Confidence: 13.8% Identity: 41% PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i Phyre2 PDB 1wv3 chain A Region: 53 - 74 Aligned: 21 Modelled: 22 Confidence: 13.6% Identity: 43% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:similar to dna segregation atpase and related PDBTitle: crystal structure of n-terminal domain of hypothetical2 protein sav0287 from staphylococcus aureus Phyre2 PDB 1hez chain D Region: 56 - 90 Aligned: 35 Modelled: 35 Confidence: 10.1% Identity: 29% PDB header:antibody Chain: D: PDB Molecule:heavy chain of ig; PDBTitle: antibody-antigen complex Phyre2 PDB 2vky chain B Region: 23 - 36 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:viral protein Chain: B: PDB Molecule:tail protein, piigcn4; PDBTitle: headbinding domain of phage p22 tailspike c-terminally2 fused to isoleucine zipper piigcn4 (chimera i) Phyre2 PDB 3i9h chain B Region: 46 - 68 Aligned: 23 Modelled: 23 Confidence: 8.3% Identity: 26% PDB header:metal binding protein Chain: B: PDB Molecule:beta and gamma crystallin; PDBTitle: crystal structure of a betagamma-crystallin domain from2 clostridium beijerinckii Phyre2 PDB 3dvg chain B domain 1 Region: 65 - 90 Aligned: 26 Modelled: 26 Confidence: 7.5% Identity: 23% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2orm chain A Region: 30 - 41 Aligned: 12 Modelled: 12 Confidence: 7.3% Identity: 33% PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase hp0924; PDBTitle: crystal structure of the 4-oxalocrotonate tautomerase homologue dmpi2 from helicobacter pylori. Phyre2 PDB 1adq chain H domain 1 Region: 57 - 90 Aligned: 34 Modelled: 34 Confidence: 6.5% Identity: 24% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1ed7 chain A Region: 53 - 71 Aligned: 19 Modelled: 19 Confidence: 6.3% Identity: 21% Fold: WW domain-like Superfamily: Carbohydrate binding domain Family: Carbohydrate binding domain Phyre2 PDB 2ko5 chain A Region: 47 - 55 Aligned: 9 Modelled: 9 Confidence: 5.9% Identity: 11% PDB header:transcription Chain: A: PDB Molecule:ring finger protein z; PDBTitle: nmr solution structure of lfv-z Phyre2 1 c2wy3B_ 2 c2o01I_ 3 c2rkzD_ 4 d1zuea1 5 d1npsa_ 6 d1wv3a2 7 d2foka4 8 d1u5ma_ 9 d1prsa2 10 c3lw5I_ 11 c2wseI_ 12 c1wv3A_ 13 c1hezD_ 14 c2vkyB_ 15 c3i9hB_ 16 d3dvgb1 17 c2ormA_ 18 d1adqh1 19 d1ed7a_ 20 c2ko5A_ 21 22 23 24

Detailed template information

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

1 c2wy3B_ 29.3 29 PDB header:immune system/viral protein Chain: B: PDB Molecule:uncharacterized protein ul16; PDBTitle: structure of the hcmv ul16-micb complex elucidates select2 binding of a viral immunoevasin to diverse nkg2d ligands 2 c2o01I_ 29.2 41 PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 3 c2rkzD_ 27.8 25 PDB header:cell adhesion Chain: D: PDB Molecule:fibronectin; PDBTitle: crystal structure of the second and third fibronectin f12 modules in complex with a fragment of staphylococcus3 aureus fnbpa-1 4 d1zuea1 25.6 33 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 5 d1npsa_ 21.1 14 Fold:gamma-Crystallin-like Superfamily:gamma-Crystallin-like Family:Crystallins/Ca-binding development proteins 6 d1wv3a2 19.4 43 Fold:SMAD/FHA domain Superfamily:SMAD/FHA domain Family:EssC N-terminal domain-like 7 d2foka4 17.7 30 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease FokI, C-terminal (catalytic) domain 8 d1u5ma_ 16.5 39 Fold:FnI-like domain Superfamily:FnI-like domain Family:VWC domain 9 d1prsa2 14.5 9 Fold:gamma-Crystallin-like Superfamily:gamma-Crystallin-like Family:Crystallins/Ca-binding development proteins 10 c3lw5I_ 13.8 41 PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i 11 c2wseI_ 13.8 41 PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i 12 c1wv3A_ 13.6 43 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:similar to dna segregation atpase and related PDBTitle: crystal structure of n-terminal domain of hypothetical2 protein sav0287 from staphylococcus aureus 13 c1hezD_ 10.1 29 PDB header:antibody Chain: D: PDB Molecule:heavy chain of ig; PDBTitle: antibody-antigen complex 14 c2vkyB_ 9.2 29 PDB header:viral protein Chain: B: PDB Molecule:tail protein, piigcn4; PDBTitle: headbinding domain of phage p22 tailspike c-terminally2 fused to isoleucine zipper piigcn4 (chimera i) 15 c3i9hB_ 8.3 26 PDB header:metal binding protein Chain: B: PDB Molecule:beta and gamma crystallin; PDBTitle: crystal structure of a betagamma-crystallin domain from2 clostridium beijerinckii 16 d3dvgb1 7.5 23 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 17 c2ormA_ 7.3 33 PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase hp0924; PDBTitle: crystal structure of the 4-oxalocrotonate tautomerase homologue dmpi2 from helicobacter pylori. 18 d1adqh1 6.5 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 19 d1ed7a_ 6.3 21 Fold:WW domain-like Superfamily:Carbohydrate binding domain Family:Carbohydrate binding domain 20 c2ko5A_ 5.9 11 PDB header:transcription Chain: A: PDB Molecule:ring finger protein z; PDBTitle: nmr solution structure of lfv-z 21 c1prrA_ not modelled 5.9 14 PDB header:binding protein Chain: A: PDB Molecule:development-specific protein s; PDBTitle: nmr-derived three-dimensional solution structure of protein2 s complexed with calcium 22 c2b5kA_ not modelled 5.5 33 PDB header:antimicrobial protein Chain: A: PDB Molecule:polyphemusin-1; PDBTitle: pv5 nmr solution structure in dpc micelles 23 c1fokA_ not modelled 5.4 30 PDB header:hydrolase/dna Chain: A: PDB Molecule:protein (foki restriction endonucleas); PDBTitle: structure of restriction endonuclease foki bound to dna 24 d1igfh1 not modelled 5.4 27 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like)

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