Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	F	M	L	N	A	T	G	L	P	L	Q	D	L	V	F	G	A	S	V	Y	F	P	P	F	F	K	A	F	A	F	G	F	V	I	W	L	V	V	H	R	L	L	R	G	W	I	Y	A	G	D	I	W	H	P	L	L	M	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.
Sequence		L	S	L	F	A	I	C	V	C	L	A	L	A	I	L	I	A	W
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 1wig chain A domain 2 Region: 51 - 56 Aligned: 6 Modelled: 6 Confidence: 21.8% Identity: 67% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2kaf chain A Region: 45 - 52 Aligned: 8 Modelled: 8 Confidence: 7.7% Identity: 50% PDB header:viral protein, rna binding protein Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: solution structure of the sars-unique domain-c from the2 nonstructural protein 3 (nsp3) of the severe acute3 respiratory syndrome coronavirus Phyre2 PDB 1vps chain A Region: 45 - 56 Aligned: 12 Modelled: 12 Confidence: 6.6% Identity: 42% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Group I dsDNA viruses Family: Papovaviridae-like VP Phyre2 PDB 2rmz chain A Region: 61 - 78 Aligned: 18 Modelled: 18 Confidence: 6.2% Identity: 33% PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: bicelle-embedded integrin beta3 transmembrane segment Phyre2 PDB 1nau chain A Region: 31 - 39 Aligned: 9 Modelled: 9 Confidence: 6.0% Identity: 56% PDB header:hormone/growth factor Chain: A: PDB Molecule:glucagon; PDBTitle: nmr solution structure of the glucagon antagonist [deshis1,2 desphe6, glu9]glucagon amide in the presence of3 perdeuterated dodecylphosphocholine micelles Phyre2 PDB 1x7d chain A Region: 4 - 22 Aligned: 19 Modelled: 19 Confidence: 5.8% Identity: 21% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Ornithine cyclodeaminase-like Phyre2 PDB 3ost chain A Region: 40 - 47 Aligned: 8 Modelled: 8 Confidence: 5.5% Identity: 63% PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p Phyre2 1 d1wiga2 2 c2kafA_ 3 d1vpsa_ 4 c2rmzA_ 5 c1nauA_ 6 d1x7da_ 7 c3ostA_

Detailed template information

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

1 d1wiga2 21.8 67 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 2 c2kafA_ 7.7 50 PDB header:viral protein, rna binding protein Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: solution structure of the sars-unique domain-c from the2 nonstructural protein 3 (nsp3) of the severe acute3 respiratory syndrome coronavirus 3 d1vpsa_ 6.6 42 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group I dsDNA viruses Family:Papovaviridae-like VP 4 c2rmzA_ 6.2 33 PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: bicelle-embedded integrin beta3 transmembrane segment 5 c1nauA_ 6.0 56 PDB header:hormone/growth factor Chain: A: PDB Molecule:glucagon; PDBTitle: nmr solution structure of the glucagon antagonist [deshis1,2 desphe6, glu9]glucagon amide in the presence of3 perdeuterated dodecylphosphocholine micelles 6 d1x7da_ 5.8 21 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Ornithine cyclodeaminase-like 7 c3ostA_ 5.5 63 PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p

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