Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	M	K	N	C	L	L	L	G	A	L	L	M	G	F	T	G	V	A	M	A	Q	S	V	T	V	D	V	P	S	G	Y	K	V	V	V	V	P	D	S	V	S	V	P	Q	A	V	S	V	A	T	V	P	Q	T	V	Y	V	A
Secondary structure
SS confidence
Disorder		?	?	?	?																																				?			?	?		?				?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.
Sequence		P	A	P	A	P	A	Y	R	P	H	P	Y	V	R	H	L	A	S	V	G	E	G	M	V	I	E	H	Q	I	D	D	H	H	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 2kyw chain A Region: 25 - 94 Aligned: 51 Modelled: 56 Confidence: 43.0% Identity: 31% PDB header:cell adhesion Chain: A: PDB Molecule:adhesion exoprotein; PDBTitle: solution nmr structure of a domain of adhesion exoprotein from2 pediococcus pentosaceus, northeast structural genomics consortium3 target ptr41o Phyre2 PDB 1zy3 chain B Region: 73 - 83 Aligned: 11 Modelled: 11 Confidence: 28.4% Identity: 64% PDB header:apoptosis Chain: B: PDB Molecule:bh3-peptide from bh3 interacting domain death PDBTitle: structural model of complex of bcl-w protein with bid bh3-2 peptide Phyre2 PDB 2oy7 chain A Region: 24 - 55 Aligned: 32 Modelled: 32 Confidence: 16.8% Identity: 38% PDB header:membrane protein Chain: A: PDB Molecule:outer surface protein a; PDBTitle: the crystal structure of ospa mutant Phyre2 PDB 2voi chain B Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 16.0% Identity: 50% PDB header:apoptosis Chain: B: PDB Molecule:bh3-interacting domain death agonist p13; PDBTitle: structure of mouse a1 bound to the bid bh3-domain Phyre2 PDB 1erf chain A Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 11.5% Identity: 58% PDB header:viral protein Chain: A: PDB Molecule:transmembrane glycoprotein; PDBTitle: conformational mapping of the n-terminal fusion peptide of2 hiv-1 gp41 using 13c-enhanced fourier transform infrared3 spectroscopy (ftir) Phyre2 PDB 2pjv chain A Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 11.2% Identity: 58% PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein; PDBTitle: solution structure of hiv-1 gp41 fusion domain bound to dpc2 micelle Phyre2 PDB 3kd4 chain A Region: 24 - 44 Aligned: 21 Modelled: 21 Confidence: 10.6% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:putative protease; PDBTitle: crystal structure of a putative protease (bdi_1141) from2 parabacteroides distasonis atcc 8503 at 2.00 a resolution Phyre2 PDB 1kwg chain A domain 3 Region: 31 - 40 Aligned: 10 Modelled: 10 Confidence: 8.2% Identity: 50% Fold: Flavodoxin-like Superfamily: Class I glutamine amidotransferase-like Family: A4 beta-galactosidase middle domain Phyre2 PDB 2jpw chain A Region: 61 - 72 Aligned: 12 Modelled: 12 Confidence: 6.7% Identity: 58% PDB header:contractile protein Chain: A: PDB Molecule:troponin i, cardiac muscle; PDBTitle: solution structure of the bisphosphorylated cardiac2 specific n-extension of cardiac troponin i Phyre2 PDB 1jzt chain A Region: 25 - 33 Aligned: 9 Modelled: 9 Confidence: 6.1% Identity: 67% Fold: YjeF N-terminal domain-like Superfamily: YjeF N-terminal domain-like Family: YjeF N-terminal domain-like Phyre2 PDB 2wto chain B Region: 11 - 44 Aligned: 34 Modelled: 34 Confidence: 6.1% Identity: 29% PDB header:metal binding protein Chain: B: PDB Molecule:orf131 protein; PDBTitle: crystal structure of apo-form czce from c. metallidurans ch34 Phyre2 PDB 2zkr chain 9 Region: 30 - 38 Aligned: 9 Modelled: 9 Confidence: 6.0% Identity: 44% PDB header:ribosomal protein/rna Chain: 9: PDB Molecule:60s ribosomal protein l32; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 2ari chain A Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 5.6% Identity: 58% PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41 Phyre2 1 c2kywA_ 2 c1zy3B_ 3 c2oy7A_ 4 c2voiB_ 5 c1erfA_ 6 c2pjvA_ 7 c3kd4A_ 8 d1kwga3 9 c2jpwA_ 10 d1jzta_ 11 c2wtoB_ 12 c2zkr9_ 13 c2ariA_

Detailed template information

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

1 c2kywA_ 43.0 31 PDB header:cell adhesion Chain: A: PDB Molecule:adhesion exoprotein; PDBTitle: solution nmr structure of a domain of adhesion exoprotein from2 pediococcus pentosaceus, northeast structural genomics consortium3 target ptr41o 2 c1zy3B_ 28.4 64 PDB header:apoptosis Chain: B: PDB Molecule:bh3-peptide from bh3 interacting domain death PDBTitle: structural model of complex of bcl-w protein with bid bh3-2 peptide 3 c2oy7A_ 16.8 38 PDB header:membrane protein Chain: A: PDB Molecule:outer surface protein a; PDBTitle: the crystal structure of ospa mutant 4 c2voiB_ 16.0 50 PDB header:apoptosis Chain: B: PDB Molecule:bh3-interacting domain death agonist p13; PDBTitle: structure of mouse a1 bound to the bid bh3-domain 5 c1erfA_ 11.5 58 PDB header:viral protein Chain: A: PDB Molecule:transmembrane glycoprotein; PDBTitle: conformational mapping of the n-terminal fusion peptide of2 hiv-1 gp41 using 13c-enhanced fourier transform infrared3 spectroscopy (ftir) 6 c2pjvA_ 11.2 58 PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein; PDBTitle: solution structure of hiv-1 gp41 fusion domain bound to dpc2 micelle 7 c3kd4A_ 10.6 19 PDB header:hydrolase Chain: A: PDB Molecule:putative protease; PDBTitle: crystal structure of a putative protease (bdi_1141) from2 parabacteroides distasonis atcc 8503 at 2.00 a resolution 8 d1kwga3 8.2 50 Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:A4 beta-galactosidase middle domain 9 c2jpwA_ 6.7 58 PDB header:contractile protein Chain: A: PDB Molecule:troponin i, cardiac muscle; PDBTitle: solution structure of the bisphosphorylated cardiac2 specific n-extension of cardiac troponin i 10 d1jzta_ 6.1 67 Fold:YjeF N-terminal domain-like Superfamily:YjeF N-terminal domain-like Family:YjeF N-terminal domain-like 11 c2wtoB_ 6.1 29 PDB header:metal binding protein Chain: B: PDB Molecule:orf131 protein; PDBTitle: crystal structure of apo-form czce from c. metallidurans ch34 12 c2zkr9_ 6.0 44 PDB header:ribosomal protein/rna Chain: 9: PDB Molecule:60s ribosomal protein l32; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 13 c2ariA_ 5.6 58 PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41

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