Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	V	F	I	C	A	A	I	P	D	E	L	A	T	R	E	E	G	A	V	A	V	A	T	A	I	E	A	G	D	E	R	R	A	R	A	K	F	H	W	Q	F	L	E	H	Y	P	A	A	Q	D	C	A	Y	K	F	I	V
Secondary structure
SS confidence
Disorder		?	?	?	?									?			?	?	?	?													?																		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		C	E	D	K	P	G	I	P	R	P	A	L	D	S	W	D	A	E	Y	M	Q	E	N	R	W	D	E	E	S	A	S	F	V	P	V	E	T	E	S	D	P	M	N	V	T	F	D	K	L	A	P	E	V	Q	N	A	V	M	V	K
Secondary structure
SS confidence
Disorder					?	?				?															?				?	?						?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	D	T	C	E	N	I	T	V	D	M	V	I	S	A	Q	E	L	L	Q	E	D	M	A	T	F	D	G	H	I	V	E	A	L	M	K	M	P	E	V	N	A	M	Y	P	E	L	K	L	H	A	I	G	W	V	K	H	K	C	I
Secondary structure
SS confidence
Disorder																					?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	G	A	K	W	P	E	I	Q	A	E	M	R	I	W	K	K	R	R	E	G	E	R	K	E	T	G	K	Y	T	S	V	V	D	L	A	R	A	R	A	N	Q	Q	Y	T	E	N	S	T	G	K	I	S	P	V	I	A	A	I	H
Secondary structure
SS confidence
Disorder					?														?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.
Sequence		R	E	Y	K	Q	T	W	K	T	L	D	D	E	L	A
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 1n7o chain A domain 1 Region: 117 - 241 Aligned: 114 Modelled: 125 Confidence: 69.9% Identity: 11% Fold: alpha/alpha toroid Superfamily: Chondroitin AC/alginate lyase Family: Hyaluronate lyase-like catalytic, N-terminal domain Phyre2 PDB 2d0t chain A domain 1 Region: 69 - 228 Aligned: 143 Modelled: 151 Confidence: 49.8% Identity: 12% Fold: Indolic compounds 2,3-dioxygenase-like Superfamily: Indolic compounds 2,3-dioxygenase-like Family: Indoleamine 2,3-dioxygenase-like Phyre2 PDB 1kyf chain A domain 1 Region: 66 - 79 Aligned: 14 Modelled: 14 Confidence: 33.3% Identity: 29% Fold: Immunoglobulin-like beta-sandwich Superfamily: Clathrin adaptor appendage domain Family: Alpha-adaptin ear subdomain-like Phyre2 PDB 1rwh chain A domain 1 Region: 117 - 200 Aligned: 83 Modelled: 84 Confidence: 32.2% Identity: 10% Fold: alpha/alpha toroid Superfamily: Chondroitin AC/alginate lyase Family: Hyaluronate lyase-like catalytic, N-terminal domain Phyre2 PDB 1qys chain A Region: 13 - 43 Aligned: 31 Modelled: 30 Confidence: 26.2% Identity: 19% PDB header:de novo protein Chain: A: PDB Molecule:top7; PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold Phyre2 PDB 1f1s chain A domain 1 Region: 117 - 200 Aligned: 83 Modelled: 84 Confidence: 23.7% Identity: 5% Fold: alpha/alpha toroid Superfamily: Chondroitin AC/alginate lyase Family: Hyaluronate lyase-like catalytic, N-terminal domain Phyre2 PDB 2jvf chain A Region: 13 - 43 Aligned: 31 Modelled: 31 Confidence: 19.1% Identity: 26% PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein Phyre2 PDB 1e85 chain A Region: 33 - 67 Aligned: 35 Modelled: 35 Confidence: 19.0% Identity: 3% Fold: Four-helical up-and-down bundle Superfamily: Cytochromes Family: Cytochrome c'-like Phyre2 PDB 1mqv chain A Region: 33 - 67 Aligned: 35 Modelled: 35 Confidence: 18.5% Identity: 20% Fold: Four-helical up-and-down bundle Superfamily: Cytochromes Family: Cytochrome c'-like Phyre2 PDB 2nr7 chain A domain 1 Region: 117 - 204 Aligned: 83 Modelled: 88 Confidence: 18.3% Identity: 20% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: NMB1012-like Phyre2 PDB 1x1i chain A domain 1 Region: 112 - 200 Aligned: 88 Modelled: 89 Confidence: 17.5% Identity: 6% Fold: alpha/alpha toroid Superfamily: Chondroitin AC/alginate lyase Family: Hyaluronate lyase-like catalytic, N-terminal domain Phyre2 PDB 1ky6 chain A Region: 66 - 79 Aligned: 14 Modelled: 14 Confidence: 15.1% Identity: 29% PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:alpha-adaptin c; PDBTitle: ap-2 clathrin adaptor alpha-appendage in complex with epsin2 dpw peptide Phyre2 PDB 3zri chain A Region: 98 - 198 Aligned: 90 Modelled: 101 Confidence: 13.2% Identity: 13% PDB header:chaperone Chain: A: PDB Molecule:clpb protein; PDBTitle: n-domain of clpv from vibrio cholerae Phyre2 PDB 2j8w chain A domain 1 Region: 33 - 67 Aligned: 35 Modelled: 35 Confidence: 12.5% Identity: 17% Fold: Four-helical up-and-down bundle Superfamily: Cytochromes Family: Cytochrome c'-like Phyre2 PDB 1gqa chain A Region: 33 - 67 Aligned: 35 Modelled: 35 Confidence: 12.4% Identity: 23% Fold: Four-helical up-and-down bundle Superfamily: Cytochromes Family: Cytochrome c'-like Phyre2 PDB 2c2x chain B Region: 125 - 216 Aligned: 90 Modelled: 92 Confidence: 11.5% Identity: 11% PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase- PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis Phyre2 PDB 2ckc chain A Region: 190 - 210 Aligned: 21 Modelled: 21 Confidence: 10.7% Identity: 14% PDB header:hydrolase Chain: A: PDB Molecule:chromodomain-helicase-dna-binding protein 7; PDBTitle: solution structures of the brk domains of the human chromo2 helicase domain 7 and 8, reveals structural similarity3 with gyf domain suggesting a role in protein interaction Phyre2 PDB 2ckc chain A domain 1 Region: 190 - 210 Aligned: 21 Modelled: 21 Confidence: 10.7% Identity: 14% Fold: GYF/BRK domain-like Superfamily: BRK domain-like Family: BRK domain-like Phyre2 PDB 1q2i chain A Region: 182 - 201 Aligned: 20 Modelled: 20 Confidence: 10.1% Identity: 20% PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells Phyre2 PDB 1t57 chain A Region: 49 - 70 Aligned: 21 Modelled: 22 Confidence: 9.0% Identity: 29% Fold: Pyruvate kinase C-terminal domain-like Superfamily: PK C-terminal domain-like Family: MTH1675-like Phyre2 1 d1n7oa1 2 d2d0ta1 3 d1kyfa1 4 d1rwha1 5 c1qysA_ 6 d1f1sa1 7 c2jvfA_ 8 d1e85a_ 9 d1mqva_ 10 d2nr7a1 11 d1x1ia1 12 c1ky6A_ 13 c3zriA_ 14 d2j8wa1 15 d1gqaa_ 16 c2c2xB_ 17 c2ckcA_ 18 d2ckca1 19 c1q2iA_ 20 d1t57a_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

Detailed template information

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

1 d1n7oa1 69.9 11 Fold:alpha/alpha toroid Superfamily:Chondroitin AC/alginate lyase Family:Hyaluronate lyase-like catalytic, N-terminal domain 2 d2d0ta1 49.8 12 Fold:Indolic compounds 2,3-dioxygenase-like Superfamily:Indolic compounds 2,3-dioxygenase-like Family:Indoleamine 2,3-dioxygenase-like 3 d1kyfa1 33.3 29 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:Alpha-adaptin ear subdomain-like 4 d1rwha1 32.2 10 Fold:alpha/alpha toroid Superfamily:Chondroitin AC/alginate lyase Family:Hyaluronate lyase-like catalytic, N-terminal domain 5 c1qysA_ 26.2 19 PDB header:de novo protein Chain: A: PDB Molecule:top7; PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold 6 d1f1sa1 23.7 5 Fold:alpha/alpha toroid Superfamily:Chondroitin AC/alginate lyase Family:Hyaluronate lyase-like catalytic, N-terminal domain 7 c2jvfA_ 19.1 26 PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein 8 d1e85a_ 19.0 3 Fold:Four-helical up-and-down bundle Superfamily:Cytochromes Family:Cytochrome c'-like 9 d1mqva_ 18.5 20 Fold:Four-helical up-and-down bundle Superfamily:Cytochromes Family:Cytochrome c'-like 10 d2nr7a1 18.3 20 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:NMB1012-like 11 d1x1ia1 17.5 6 Fold:alpha/alpha toroid Superfamily:Chondroitin AC/alginate lyase Family:Hyaluronate lyase-like catalytic, N-terminal domain 12 c1ky6A_ 15.1 29 PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:alpha-adaptin c; PDBTitle: ap-2 clathrin adaptor alpha-appendage in complex with epsin2 dpw peptide 13 c3zriA_ 13.2 13 PDB header:chaperone Chain: A: PDB Molecule:clpb protein; PDBTitle: n-domain of clpv from vibrio cholerae 14 d2j8wa1 12.5 17 Fold:Four-helical up-and-down bundle Superfamily:Cytochromes Family:Cytochrome c'-like 15 d1gqaa_ 12.4 23 Fold:Four-helical up-and-down bundle Superfamily:Cytochromes Family:Cytochrome c'-like 16 c2c2xB_ 11.5 11 PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase- PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis 17 c2ckcA_ 10.7 14 PDB header:hydrolase Chain: A: PDB Molecule:chromodomain-helicase-dna-binding protein 7; PDBTitle: solution structures of the brk domains of the human chromo2 helicase domain 7 and 8, reveals structural similarity3 with gyf domain suggesting a role in protein interaction 18 d2ckca1 10.7 14 Fold:GYF/BRK domain-like Superfamily:BRK domain-like Family:BRK domain-like 19 c1q2iA_ 10.1 20 PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells 20 d1t57a_ 9.0 29 Fold:Pyruvate kinase C-terminal domain-like Superfamily:PK C-terminal domain-like Family:MTH1675-like 21 d1s0pa_ not modelled 8.9 18 Fold:N-terminal domain of adenylylcyclase associated protein, CAP Superfamily:N-terminal domain of adenylylcyclase associated protein, CAP Family:N-terminal domain of adenylylcyclase associated protein, CAP 22 d1b6aa1 not modelled 8.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Methionine aminopeptidase, insert domain 23 d1s05a_ not modelled 7.9 4 Fold:Four-helical up-and-down bundle Superfamily:Cytochromes Family:Cytochrome c'-like 24 d3e2ba1 not modelled 7.2 14 Fold:DLC Superfamily:DLC Family:DLC 25 d2ikba1 not modelled 6.9 10 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:NMB1012-like 26 d1hdma2 not modelled 6.9 22 Fold:MHC antigen-recognition domain Superfamily:MHC antigen-recognition domain Family:MHC antigen-recognition domain 27 c3ajfA_ not modelled 6.4 22 PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: structural insigths into dsrna binding and rna silencing suppression2 by ns3 protein of rice hoja blanca tenuivirus 28 d1pwka_ not modelled 6.3 11 Fold:DLC Superfamily:DLC Family:DLC 29 d1k8ia2 not modelled 6.2 22 Fold:MHC antigen-recognition domain Superfamily:MHC antigen-recognition domain Family:MHC antigen-recognition domain 30 c2o35A_ not modelled 6.2 38 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein duf1244; PDBTitle: protein of unknown function (duf1244) from sinorhizobium meliloti 31 d2o35a1 not modelled 6.2 38 Fold:SMc04008-like Superfamily:SMc04008-like Family:SMc04008-like 32 d1u69a_ not modelled 6.1 44 Fold:Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Superfamily:Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Family:3-demethylubiquinone-9 3-methyltransferase 33 d1vkma_ not modelled 6.1 25 Fold:Indigoidine synthase A-like Superfamily:Indigoidine synthase A-like Family:Indigoidine synthase A-like 34 d2f53d2 not modelled 6.0 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C1 set domains (antibody constant domain-like) 35 d1cmia_ not modelled 5.8 11 Fold:DLC Superfamily:DLC Family:DLC 36 d1vp8a_ not modelled 5.8 21 Fold:Pyruvate kinase C-terminal domain-like Superfamily:PK C-terminal domain-like Family:MTH1675-like 37 d2bnqd2 not modelled 5.8 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C1 set domains (antibody constant domain-like) 38 d1cpqa_ not modelled 5.7 13 Fold:Four-helical up-and-down bundle Superfamily:Cytochromes Family:Cytochrome c'-like 39 c3fybA_ not modelled 5.5 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein of unknown function (duf1244); PDBTitle: crystal structure of a protein of unknown function (duf1244) from2 alcanivorax borkumensis 40 d2foka4 not modelled 5.3 17 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease FokI, C-terminal (catalytic) domain 41 c2vuxB_ not modelled 5.2 14 PDB header:oxidoreductase Chain: B: PDB Molecule:ribonucleoside-diphosphate reductase subunit m2 b; PDBTitle: human ribonucleotide reductase, subunit m2 b

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