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

T

A

K

E

Y

S

D

T

A

K

R

E

V

S

V

D

V

D

A

L

L

A

A

I

N

E

I

S

E

S

E

V

H

R

S

Q

N

D

S

E

H

V

S

V

D

G

R

E

Y

H

T

W

R

E

L

A

D

A

Secondary structure

SS confidence

Disorder

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?

?

?

?

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?

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?

?

?

?

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?

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?

Disorder confidence

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70

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Sequence

F

E

L

D

I

H

D

F

S

V

S

E

V

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

PDB 3sak chain A Region: 49 - 63 Aligned: 15 Modelled: 15 Confidence: 24.7% Identity: 40% Fold: p53 tetramerization domain Superfamily: p53 tetramerization domain Family: p53 tetramerization domain Phyre2 PDB 2j10 chain B Region: 50 - 63 Aligned: 14 Modelled: 14 Confidence: 23.0% Identity: 43% PDB header:transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k Phyre2 PDB 2j10 chain D Region: 50 - 63 Aligned: 14 Modelled: 14 Confidence: 23.0% Identity: 43% PDB header:transcription Chain: D: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k Phyre2 PDB 2j10 chain A Region: 50 - 63 Aligned: 14 Modelled: 14 Confidence: 23.0% Identity: 43% PDB header:transcription Chain: A: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k Phyre2 PDB 1aie chain A Region: 50 - 69 Aligned: 20 Modelled: 20 Confidence: 17.1% Identity: 30% Fold: p53 tetramerization domain Superfamily: p53 tetramerization domain Family: p53 tetramerization domain Phyre2 PDB 2j11 chain D Region: 50 - 69 Aligned: 20 Modelled: 20 Confidence: 15.5% Identity: 30% PDB header:transcription Chain: D: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant y327s t329g q331g Phyre2 PDB 2k53 chain A Region: 11 - 33 Aligned: 23 Modelled: 23 Confidence: 11.0% Identity: 30% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 Phyre2 PDB 2k5e chain A Region: 9 - 35 Aligned: 27 Modelled: 27 Confidence: 10.2% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of putative uncharacterized protein2 gsu1278 from methanocaldococcus jannaschii, northeast3 structural genomics consortium (nesg) target gsr195 Phyre2 PDB 1qp8 chain A Region: 1 - 68 Aligned: 67 Modelled: 67 Confidence: 10.1% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:formate dehydrogenase; PDBTitle: crystal structure of a putative formate dehydrogenase from2 pyrobaculum aerophilum Phyre2 PDB 2vzd chain D Region: 18 - 27 Aligned: 10 Modelled: 10 Confidence: 8.3% Identity: 60% PDB header:cell adhesion Chain: D: PDB Molecule:paxillin; PDBTitle: crystal structure of the c-terminal calponin homology2 domain of alpha parvin in complex with paxillin ld1 motif Phyre2 PDB 2vzd chain C Region: 18 - 27 Aligned: 10 Modelled: 10 Confidence: 8.2% Identity: 60% PDB header:cell adhesion Chain: C: PDB Molecule:paxillin; PDBTitle: crystal structure of the c-terminal calponin homology2 domain of alpha parvin in complex with paxillin ld1 motif Phyre2 PDB 2o8r chain A domain 3 Region: 2 - 26 Aligned: 25 Modelled: 25 Confidence: 7.1% Identity: 40% Fold: Phospholipase D/nuclease Superfamily: Phospholipase D/nuclease Family: Polyphosphate kinase C-terminal domain Phyre2 PDB 1a1u chain A Region: 50 - 63 Aligned: 14 Modelled: 14 Confidence: 6.9% Identity: 36% Fold: p53 tetramerization domain Superfamily: p53 tetramerization domain Family: p53 tetramerization domain Phyre2 PDB 1dxy chain A Region: 1 - 68 Aligned: 65 Modelled: 68 Confidence: 6.3% Identity: 20% PDB header:oxidoreductase Chain: A: PDB Molecule:d-2-hydroxyisocaproate dehydrogenase; PDBTitle: structure of d-2-hydroxyisocaproate dehydrogenase Phyre2 PDB 1a6d chain A domain 3 Region: 21 - 33 Aligned: 13 Modelled: 13 Confidence: 6.3% Identity: 31% Fold: GroEL-intermediate domain like Superfamily: GroEL-intermediate domain like Family: Group II chaperonin (CCT, TRIC), intermediate domain Phyre2 PDB 2o8r chain A Region: 2 - 60 Aligned: 59 Modelled: 59 Confidence: 6.2% Identity: 22% PDB header:transferase Chain: A: PDB Molecule:polyphosphate kinase; PDBTitle: crystal structure of polyphosphate kinase from2 porphyromonas gingivalis Phyre2 PDB 2gno chain A domain 1 Region: 51 - 61 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 45% Fold: post-AAA+ oligomerization domain-like Superfamily: post-AAA+ oligomerization domain-like Family: DNA polymerase III clamp loader subunits, C-terminal domain Phyre2 1 d3saka_ 2 c2j10B_ 3 c2j10D_ 4 c2j10A_ 5 d1aiea_ 6 c2j11D_ 7 c2k53A_ 8 c2k5eA_ 9 c1qp8A_ 10 c2vzdD_ 11 c2vzdC_ 12 d2o8ra3 13 d1a1ua_ 14 c1dxyA_ 15 d1a6da3 16 c2o8rA_ 17 d2gnoa1

Detailed template information

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

1 d3saka_ 24.7 40 Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain 2 c2j10B_ 23.0 43 PDB header:transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k 3 c2j10D_ 23.0 43 PDB header:transcription Chain: D: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k 4 c2j10A_ 23.0 43 PDB header:transcription Chain: A: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k 5 d1aiea_ 17.1 30 Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain 6 c2j11D_ 15.5 30 PDB header:transcription Chain: D: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant y327s t329g q331g 7 c2k53A_ 11.0 30 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 8 c2k5eA_ 10.2 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of putative uncharacterized protein2 gsu1278 from methanocaldococcus jannaschii, northeast3 structural genomics consortium (nesg) target gsr195 9 c1qp8A_ 10.1 15 PDB header:oxidoreductase Chain: A: PDB Molecule:formate dehydrogenase; PDBTitle: crystal structure of a putative formate dehydrogenase from2 pyrobaculum aerophilum 10 c2vzdD_ 8.3 60 PDB header:cell adhesion Chain: D: PDB Molecule:paxillin; PDBTitle: crystal structure of the c-terminal calponin homology2 domain of alpha parvin in complex with paxillin ld1 motif 11 c2vzdC_ 8.2 60 PDB header:cell adhesion Chain: C: PDB Molecule:paxillin; PDBTitle: crystal structure of the c-terminal calponin homology2 domain of alpha parvin in complex with paxillin ld1 motif 12 d2o8ra3 7.1 40 Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:Polyphosphate kinase C-terminal domain 13 d1a1ua_ 6.9 36 Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain 14 c1dxyA_ 6.3 20 PDB header:oxidoreductase Chain: A: PDB Molecule:d-2-hydroxyisocaproate dehydrogenase; PDBTitle: structure of d-2-hydroxyisocaproate dehydrogenase 15 d1a6da3 6.3 31 Fold:GroEL-intermediate domain like Superfamily:GroEL-intermediate domain like Family:Group II chaperonin (CCT, TRIC), intermediate domain 16 c2o8rA_ 6.2 22 PDB header:transferase Chain: A: PDB Molecule:polyphosphate kinase; PDBTitle: crystal structure of polyphosphate kinase from2 porphyromonas gingivalis 17 d2gnoa1 5.5 45 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal 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

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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