Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	H	L	D	E	V	I	A	R	V	D	A	A	I	E	E	S	V	I	A	H	M	N	E	L	L	I	A	L	S	D	D	A	E	L	S	R	E	D	R	Y	T	Q	Q	Q	R	L	R	T	A	I	A	H	H	G	R	K	H	K
Secondary structure
SS confidence
Disorder		?	?	?																																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.
Sequence		E	D	M	E	A	R	H	E	Q	L	T	K	G	G	T	I	L
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 3bt6 chain B Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 17.8% Identity: 25% PDB header:viral protein Chain: B: PDB Molecule:influenza b hemagglutinin (ha); PDBTitle: crystal structure of influenza b virus hemagglutinin Phyre2 PDB 1htm chain B Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 16.1% Identity: 28% PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: structure of influenza haemagglutinin at the ph of membrane2 fusion Phyre2 PDB 1ru7 chain B Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 15.2% Identity: 20% PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin; PDBTitle: 1934 human h1 hemagglutinin Phyre2 PDB 2wr2 chain B Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 14.7% Identity: 23% PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin; PDBTitle: structure of influenza h2 avian hemagglutinin with avian2 receptor Phyre2 PDB 1jsd chain B Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 12.1% Identity: 23% PDB header:viral protein Chain: B: PDB Molecule:haemagglutinin (ha2 chain); PDBTitle: crystal structure of swine h9 haemagglutinin Phyre2 PDB 3m5g chain D Region: 2 - 40 Aligned: 38 Modelled: 39 Confidence: 10.9% Identity: 24% PDB header:viral protein Chain: D: PDB Molecule:hemagglutinin; PDBTitle: crystal structure of a h7 influenza virus hemagglutinin Phyre2 PDB 2wrh chain I Region: 2 - 40 Aligned: 38 Modelled: 39 Confidence: 10.2% Identity: 24% PDB header:viral protein Chain: I: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: structure of h1 duck albert hemagglutinin with human2 receptor Phyre2 PDB 1t6u chain A Region: 13 - 39 Aligned: 27 Modelled: 27 Confidence: 8.5% Identity: 22% Fold: Four-helical up-and-down bundle Superfamily: Nickel-containing superoxide dismutase, NiSOD Family: Nickel-containing superoxide dismutase, NiSOD Phyre2 PDB 1mql chain B Region: 2 - 40 Aligned: 38 Modelled: 39 Confidence: 8.5% Identity: 18% PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: bha of ukr/63 Phyre2 PDB 1reg chain X Region: 20 - 40 Aligned: 21 Modelled: 21 Confidence: 6.5% Identity: 33% Fold: Ferredoxin-like Superfamily: Translational regulator protein regA Family: Translational regulator protein regA Phyre2 PDB 1hge chain D Region: 2 - 40 Aligned: 38 Modelled: 39 Confidence: 6.5% Identity: 18% PDB header:viral protein Chain: D: PDB Molecule:hemagglutinin, (g135r), ha1 chain; PDBTitle: binding of influenza virus hemagglutinin to analogs of its cell-2 surface receptor, sialic acid: analysis by proton nuclear magnetic3 resonance spectroscopy and x-ray crystallography Phyre2 PDB 2rmi chain A Region: 60 - 70 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 64% PDB header:neuropeptide Chain: A: PDB Molecule:astressin; PDBTitle: 3d nmr structure of astressin Phyre2 PDB 1ha0 chain A Region: 2 - 40 Aligned: 38 Modelled: 39 Confidence: 6.3% Identity: 18% PDB header:viral protein Chain: A: PDB Molecule:protein (hemagglutinin precursor); PDBTitle: hemagglutinin precursor ha0 Phyre2 1 c3bt6B_ 2 c1htmB_ 3 c1ru7B_ 4 c2wr2B_ 5 c1jsdB_ 6 c3m5gD_ 7 c2wrhI_ 8 d1t6ua_ 9 c1mqlB_ 10 d1regx_ 11 c1hgeD_ 12 c2rmiA_ 13 c1ha0A_

Detailed template information

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

1 c3bt6B_ 17.8 25 PDB header:viral protein Chain: B: PDB Molecule:influenza b hemagglutinin (ha); PDBTitle: crystal structure of influenza b virus hemagglutinin 2 c1htmB_ 16.1 28 PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: structure of influenza haemagglutinin at the ph of membrane2 fusion 3 c1ru7B_ 15.2 20 PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin; PDBTitle: 1934 human h1 hemagglutinin 4 c2wr2B_ 14.7 23 PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin; PDBTitle: structure of influenza h2 avian hemagglutinin with avian2 receptor 5 c1jsdB_ 12.1 23 PDB header:viral protein Chain: B: PDB Molecule:haemagglutinin (ha2 chain); PDBTitle: crystal structure of swine h9 haemagglutinin 6 c3m5gD_ 10.9 24 PDB header:viral protein Chain: D: PDB Molecule:hemagglutinin; PDBTitle: crystal structure of a h7 influenza virus hemagglutinin 7 c2wrhI_ 10.2 24 PDB header:viral protein Chain: I: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: structure of h1 duck albert hemagglutinin with human2 receptor 8 d1t6ua_ 8.5 22 Fold:Four-helical up-and-down bundle Superfamily:Nickel-containing superoxide dismutase, NiSOD Family:Nickel-containing superoxide dismutase, NiSOD 9 c1mqlB_ 8.5 18 PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: bha of ukr/63 10 d1regx_ 6.5 33 Fold:Ferredoxin-like Superfamily:Translational regulator protein regA Family:Translational regulator protein regA 11 c1hgeD_ 6.5 18 PDB header:viral protein Chain: D: PDB Molecule:hemagglutinin, (g135r), ha1 chain; PDBTitle: binding of influenza virus hemagglutinin to analogs of its cell-2 surface receptor, sialic acid: analysis by proton nuclear magnetic3 resonance spectroscopy and x-ray crystallography 12 c2rmiA_ 6.3 64 PDB header:neuropeptide Chain: A: PDB Molecule:astressin; PDBTitle: 3d nmr structure of astressin 13 c1ha0A_ 6.3 18 PDB header:viral protein Chain: A: PDB Molecule:protein (hemagglutinin precursor); PDBTitle: hemagglutinin precursor ha0

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