Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	A	I	G	K	L	P	K	G	V	L	I	L	E	F	I	G	M	M	L	L	A	V	A	L	L	S	V	S	D	S	L	S	L	P	E	P	F	S	R	P	E	V	Q	I	L	M	I	F	L	G	V	L	L	M	L	P	A	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?																										?	?			?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.
Sequence		V	V	V	I	L	Q	V	A	K	R	L	A	P	Q	L	M	N	R	P	P	Q	Y	S	R	S	E	R	E	K	D	N	D	A	N	H
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 2y69 chain Z Region: 37 - 63 Aligned: 27 Modelled: 27 Confidence: 48.1% Identity: 30% PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1v54 chain M Region: 37 - 63 Aligned: 27 Modelled: 27 Confidence: 40.3% Identity: 30% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Phyre2 PDB 2jwa chain A Region: 8 - 24 Aligned: 17 Modelled: 17 Confidence: 10.2% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 3fhg chain A Region: 26 - 87 Aligned: 59 Modelled: 62 Confidence: 9.8% Identity: 10% PDB header:dna repair, hydrolase, lyase Chain: A: PDB Molecule:n-glycosylase/dna lyase; PDBTitle: crystal structure of sulfolobus solfataricus 8-oxoguanine dna2 glycosylase (ssogg) Phyre2 PDB 3dww chain A Region: 13 - 71 Aligned: 54 Modelled: 59 Confidence: 7.9% Identity: 17% PDB header:isomerase Chain: A: PDB Molecule:prostaglandin e synthase; PDBTitle: electron crystallographic structure of human microsomal2 prostaglandin e synthase 1 Phyre2 PDB 1wu0 chain A Region: 13 - 31 Aligned: 19 Modelled: 19 Confidence: 6.0% Identity: 5% PDB header:hydrolase Chain: A: PDB Molecule:atp synthase c chain; PDBTitle: solution structure of subunit c of f1fo-atp synthase from2 the thermophilic bacillus ps3 Phyre2 PDB 2wpd chain P Region: 13 - 29 Aligned: 17 Modelled: 17 Confidence: 5.8% Identity: 29% PDB header:hydrolase Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial; PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase Phyre2 1 c2y69Z_ 2 d1v54m_ 3 c2jwaA_ 4 c3fhgA_ 5 c3dwwA_ 6 c1wu0A_ 7 c2wpdP_

Detailed template information

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

1 c2y69Z_ 48.1 30 PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 2 d1v54m_ 40.3 30 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) 3 c2jwaA_ 10.2 29 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 4 c3fhgA_ 9.8 10 PDB header:dna repair, hydrolase, lyase Chain: A: PDB Molecule:n-glycosylase/dna lyase; PDBTitle: crystal structure of sulfolobus solfataricus 8-oxoguanine dna2 glycosylase (ssogg) 5 c3dwwA_ 7.9 17 PDB header:isomerase Chain: A: PDB Molecule:prostaglandin e synthase; PDBTitle: electron crystallographic structure of human microsomal2 prostaglandin e synthase 1 6 c1wu0A_ 6.0 5 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase c chain; PDBTitle: solution structure of subunit c of f1fo-atp synthase from2 the thermophilic bacillus ps3 7 c2wpdP_ 5.8 29 PDB header:hydrolase Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial; PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase

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