Secondary structure and disorder prediction

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Sequence		M	P	D	S	R	K	A	R	R	I	A	D	P	G	L	Q	P	E	R	T	S	L	A	W	F	R	T	M	L	G	Y	G	A	L	M	A	L	A	I	K	H	N	W	H	Q	A	G	M	L	F	W	I	S	I	G	I	L	A	I	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	L	I	L	W	H	Y	T	R	N	R	N	L	M	D	V	T	N	S	D	F	S	Q	F	H	V	V	R	D	K	F	L	I	S	L	A	V	L	S	L	A	I	L	F	A	V	T	H	I	H	Q	L	I	V	F	I	E	R	V	A
Secondary structure
SS confidence
Disorder																																																										?	?	?	?
Disorder confidence
Sequence
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 3chx chain G Region: 49 - 105 Aligned: 54 Modelled: 57 Confidence: 59.5% Identity: 30% PDB header:membrane protein Chain: G: PDB Molecule:pmoc; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) Phyre2 PDB 1prt chain F Region: 23 - 40 Aligned: 17 Modelled: 18 Confidence: 51.7% Identity: 59% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Bacterial AB5 toxins, B-subunits Phyre2 PDB 1yew chain C Region: 49 - 105 Aligned: 54 Modelled: 57 Confidence: 44.7% Identity: 30% PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase Phyre2 PDB 1pjw chain A Region: 39 - 47 Aligned: 9 Modelled: 9 Confidence: 25.8% Identity: 67% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Class II viral fusion proteins C-terminal domain Phyre2 PDB 1s6n chain A Region: 39 - 47 Aligned: 9 Modelled: 9 Confidence: 24.6% Identity: 56% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Class II viral fusion proteins C-terminal domain Phyre2 PDB 3egp chain A Region: 39 - 47 Aligned: 9 Modelled: 9 Confidence: 24.6% Identity: 33% PDB header:viral protein Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure analysis of dengue-1 envelope protein2 domain iii Phyre2 PDB 3lbw chain B Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 24.3% Identity: 38% PDB header:transport protein Chain: B: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 Phyre2 PDB 3lbw chain D Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 24.3% Identity: 38% PDB header:transport protein Chain: D: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 Phyre2 PDB 3lbw chain C Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 24.3% Identity: 38% PDB header:transport protein Chain: C: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 Phyre2 PDB 3lbw chain A Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 24.3% Identity: 38% PDB header:transport protein Chain: A: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 Phyre2 PDB 1v32 chain A Region: 60 - 81 Aligned: 22 Modelled: 22 Confidence: 19.4% Identity: 23% Fold: SWIB/MDM2 domain Superfamily: SWIB/MDM2 domain Family: SWIB/MDM2 domain Phyre2 PDB 2jqm chain A Region: 39 - 47 Aligned: 9 Modelled: 9 Confidence: 18.2% Identity: 33% PDB header:transferase Chain: A: PDB Molecule:envelope protein e; PDBTitle: yellow fever envelope protein domain iii nmr structure2 (s288-k398) Phyre2 PDB 3c9j chain C Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 18.2% Identity: 38% PDB header:membrane protein Chain: C: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex Phyre2 PDB 3c9j chain B Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 18.2% Identity: 38% PDB header:membrane protein Chain: B: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex Phyre2 PDB 3c9j chain A Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 18.2% Identity: 38% PDB header:membrane protein Chain: A: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex Phyre2 PDB 3c9j chain D Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 18.2% Identity: 38% PDB header:membrane protein Chain: D: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex Phyre2 PDB 1v31 chain A Region: 60 - 78 Aligned: 19 Modelled: 19 Confidence: 17.6% Identity: 26% Fold: SWIB/MDM2 domain Superfamily: SWIB/MDM2 domain Family: SWIB/MDM2 domain Phyre2 PDB 1ixr chain A domain 1 Region: 17 - 39 Aligned: 23 Modelled: 23 Confidence: 14.6% Identity: 43% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: DNA helicase RuvA subunit, middle domain Phyre2 PDB 2h0p chain A Region: 39 - 47 Aligned: 9 Modelled: 9 Confidence: 14.0% Identity: 22% PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein; PDBTitle: nmr structure of the dengue-4 virus envelope protein domain2 iii Phyre2 PDB 1uhr chain A Region: 60 - 81 Aligned: 22 Modelled: 22 Confidence: 12.6% Identity: 27% Fold: SWIB/MDM2 domain Superfamily: SWIB/MDM2 domain Family: SWIB/MDM2 domain Phyre2 1 c3chxG_ 2 d1prtf_ 3 c1yewC_ 4 d1pjwa_ 5 d1s6na_ 6 c3egpA_ 7 c3lbwB_ 8 c3lbwD_ 9 c3lbwC_ 10 c3lbwA_ 11 d1v32a_ 12 c2jqmA_ 13 c3c9jC_ 14 c3c9jB_ 15 c3c9jA_ 16 c3c9jD_ 17 d1v31a_ 18 d1ixra1 19 c2h0pA_ 20 d1uhra_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61

Detailed template information

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

1 c3chxG_ 59.5 30 PDB header:membrane protein Chain: G: PDB Molecule:pmoc; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) 2 d1prtf_ 51.7 59 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits 3 c1yewC_ 44.7 30 PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase 4 d1pjwa_ 25.8 67 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 5 d1s6na_ 24.6 56 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 6 c3egpA_ 24.6 33 PDB header:viral protein Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure analysis of dengue-1 envelope protein2 domain iii 7 c3lbwB_ 24.3 38 PDB header:transport protein Chain: B: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 8 c3lbwD_ 24.3 38 PDB header:transport protein Chain: D: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 9 c3lbwC_ 24.3 38 PDB header:transport protein Chain: C: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 10 c3lbwA_ 24.3 38 PDB header:transport protein Chain: A: PDB Molecule:m2 protein; PDBTitle: high resolution crystal structure of transmembrane domain of m2 11 d1v32a_ 19.4 23 Fold:SWIB/MDM2 domain Superfamily:SWIB/MDM2 domain Family:SWIB/MDM2 domain 12 c2jqmA_ 18.2 33 PDB header:transferase Chain: A: PDB Molecule:envelope protein e; PDBTitle: yellow fever envelope protein domain iii nmr structure2 (s288-k398) 13 c3c9jC_ 18.2 38 PDB header:membrane protein Chain: C: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex 14 c3c9jB_ 18.2 38 PDB header:membrane protein Chain: B: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex 15 c3c9jA_ 18.2 38 PDB header:membrane protein Chain: A: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex 16 c3c9jD_ 18.2 38 PDB header:membrane protein Chain: D: PDB Molecule:proton channel protein m2, transmembrane segment; PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex 17 d1v31a_ 17.6 26 Fold:SWIB/MDM2 domain Superfamily:SWIB/MDM2 domain Family:SWIB/MDM2 domain 18 d1ixra1 14.6 43 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:DNA helicase RuvA subunit, middle domain 19 c2h0pA_ 14.0 22 PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein; PDBTitle: nmr structure of the dengue-4 virus envelope protein domain2 iii 20 d1uhra_ 12.6 27 Fold:SWIB/MDM2 domain Superfamily:SWIB/MDM2 domain Family:SWIB/MDM2 domain 21 c2kncA_ not modelled 12.1 31 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 22 d2iuba2 not modelled 11.9 17 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 23 c2wwbC_ not modelled 11.9 36 PDB header:ribosome Chain: C: PDB Molecule:protein transport protein sec61 subunit beta; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome 24 c1nyjB_ not modelled 9.6 33 PDB header:viral protein Chain: B: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 25 c2kqtC_ not modelled 9.6 33 PDB header:transport protein Chain: C: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 26 c2kqtA_ not modelled 9.6 33 PDB header:transport protein Chain: A: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 27 c1nyjA_ not modelled 9.6 33 PDB header:viral protein Chain: A: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 28 c1nyjD_ not modelled 9.6 33 PDB header:viral protein Chain: D: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 29 c2kqtB_ not modelled 9.6 33 PDB header:transport protein Chain: B: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 30 c1nyjC_ not modelled 9.6 33 PDB header:viral protein Chain: C: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 31 c1mp6A_ not modelled 9.6 33 PDB header:membrane protein Chain: A: PDB Molecule:matrix protein m2; PDBTitle: structure of the transmembrane region of the m2 protein h+2 channel by solid state nmr spectroscopy 32 c2kqtD_ not modelled 9.6 33 PDB header:transport protein Chain: D: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 33 c2bbjB_ not modelled 9.0 14 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 34 d2fp7b1 not modelled 8.3 55 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 35 c3bkdE_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: E: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 36 c3bkdG_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: G: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 37 c3bkdH_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: H: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 38 c3bkdD_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: D: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 39 c3bkdC_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: C: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 40 c3bkdA_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: A: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 41 c3bkdF_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: F: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 42 c3bkdB_ not modelled 8.1 33 PDB header:viral protein, membrane protein Chain: B: PDB Molecule:transmembrane domain of matrix protein m2; PDBTitle: high resolution crystal structure of transmembrane domain of m22 protein 43 c3c6dB_ not modelled 7.1 33 PDB header:virus Chain: B: PDB Molecule:polyprotein; PDBTitle: the pseudo-atomic structure of dengue immature virus 44 c2ehoL_ not modelled 6.8 16 PDB header:replication Chain: L: PDB Molecule:gins complex subunit 3; PDBTitle: crystal structure of human gins complex 45 c3i9yA_ not modelled 6.7 13 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the v. parahaemolyticus histidine2 kinase sensor tors sensor domain 46 d1ok8a1 not modelled 6.5 38 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 47 d2fomb1 not modelled 6.2 55 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 48 c3e90B_ not modelled 6.2 55 PDB header:hydrolase Chain: B: PDB Molecule:ns3 protease; PDBTitle: west nile vi rus ns2b-ns3protease in complexed with2 inhibitor naph-kkr-h 49 c2rlfA_ not modelled 6.2 33 PDB header:proton transport Chain: A: PDB Molecule:matrix protein 2; PDBTitle: proton channel m2 from influenza a in complex with2 inhibitor rimantadine 50 d2ijob1 not modelled 6.2 55 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 51 c3uajA_ not modelled 5.8 22 PDB header:viral protein/immune system Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure of the envelope glycoprotein ectodomain from dengue2 virus serotype 4 in complex with the fab fragment of the chimpanzee3 monoclonal antibody 5h2 52 c2w8xB_ not modelled 5.7 40 PDB header:membrane protein Chain: B: PDB Molecule:ion-channel modulator raklp; PDBTitle: structure of the tick ion-channel modulator ra-klp 53 c1urzC_ not modelled 5.6 44 PDB header:virus/viral protein Chain: C: PDB Molecule:envelope protein; PDBTitle: low ph induced, membrane fusion conformation of the2 envelope protein of tick-borne encephalitis virus 54 d2f2ab1 not modelled 5.5 39 Fold:GatB/YqeY motif Superfamily:GatB/YqeY motif Family:GatB/GatE C-terminal domain-like 55 d1befa_ not modelled 5.4 55 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 56 c3lkwA_ not modelled 5.4 55 PDB header:viral protein,hydrolase Chain: A: PDB Molecule:fusion protein of nonstructural protein 2b and PDBTitle: crystal structure of dengue virus 1 ns2b/ns3 protease active2 site mutant 57 d1ztxe1 not modelled 5.3 50 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 58 c2kadD_ not modelled 5.3 29 PDB header:membrane protein Chain: D: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 59 c2kadA_ not modelled 5.3 29 PDB header:membrane protein Chain: A: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 60 c2kadC_ not modelled 5.3 29 PDB header:membrane protein Chain: C: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 61 c2kadB_ not modelled 5.3 29 PDB header:membrane protein Chain: B: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain

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