Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	L	N	A	T	I	L	G	Q	A	I	A	F	V	L	F	V	L	F	C	M	K	Y	V	W	P	P	L	M	A	A	I	E	K	R	Q	K	E	I	A	D	G	L	A	S	A	E	R	A	H	K	D	L	D	L	A	K	A	S
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	T	D	Q	L	K	K	A	K	A	E	A	Q	V	I	I	E	Q	A	N	K	R	R	S	Q	I	L	D	E	A	K	A	E	A	E	Q	E	R	T	K	I	V	A	Q	A	Q	A	E	I	E	A	E	R	K	R	A	R	E	E	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.
Sequence		R	K	Q	V	A	I	L	A	V	A	G	A	E	K	I	I	E	R	S	V	D	E	A	A	N	S	D	I	V	D	K	L	V	A	E	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 1b9u chain A Region: 1 - 33 Aligned: 33 Modelled: 33 Confidence: 98.3% Identity: 100% PDB header:hydrolase Chain: A: PDB Molecule:protein (atp synthase); PDBTitle: membrane domain of the subunit b of the e.coli atp synthase Phyre2 PDB 1l2p chain A Region: 63 - 121 Aligned: 59 Modelled: 59 Confidence: 97.6% Identity: 100% Fold: Single transmembrane helix Superfamily: F1F0 ATP synthase subunit B, membrane domain Family: F1F0 ATP synthase subunit B, membrane domain Phyre2 PDB 3k5b chain E Region: 55 - 155 Aligned: 101 Modelled: 101 Confidence: 96.3% Identity: 19% PDB header:hydrolase Chain: E: PDB Molecule:v-type atp synthase subunit e; PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase Phyre2 PDB 2oar chain A domain 1 Region: 3 - 35 Aligned: 33 Modelled: 33 Confidence: 90.9% Identity: 24% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2oar chain A Region: 2 - 60 Aligned: 57 Modelled: 59 Confidence: 90.1% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 2khk chain A Region: 33 - 79 Aligned: 47 Modelled: 47 Confidence: 87.9% Identity: 100% PDB header:transport protein Chain: A: PDB Molecule:atp synthase subunit b; PDBTitle: nmr solution structure of the b30-82 domain of subunit b of2 escherichia coli f1fo atp synthase Phyre2 PDB 3hzq chain A Region: 2 - 31 Aligned: 29 Modelled: 30 Confidence: 81.0% Identity: 7% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state Phyre2 PDB 2rdd chain B Region: 8 - 41 Aligned: 34 Modelled: 34 Confidence: 77.0% Identity: 15% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 3k5b chain B Region: 40 - 136 Aligned: 97 Modelled: 97 Confidence: 76.3% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase, subunit (vapc-therm); PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase Phyre2 PDB 1y4c chain A Region: 40 - 156 Aligned: 115 Modelled: 117 Confidence: 70.0% Identity: 18% PDB header:de novo protein Chain: A: PDB Molecule:maltose binding protein fused with designed PDBTitle: designed helical protein fusion mbp Phyre2 PDB 1qcr chain D Region: 7 - 37 Aligned: 31 Modelled: 31 Confidence: 43.6% Identity: 6% PDB header: PDB COMPND: Phyre2 PDB 3rfr chain I Region: 1 - 30 Aligned: 30 Modelled: 30 Confidence: 37.3% Identity: 3% PDB header:oxidoreductase Chain: I: PDB Molecule:pmob; PDBTitle: crystal structure of particulate methane monooxygenase (pmmo) from2 methylocystis sp. strain m Phyre2 PDB 2k88 chain A Region: 65 - 108 Aligned: 44 Modelled: 44 Confidence: 33.0% Identity: 34% PDB header:hydrolase Chain: A: PDB Molecule:vacuolar proton pump subunit g; PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase Phyre2 PDB 3dtu chain B domain 2 Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 24.9% Identity: 16% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1jdm chain A Region: 1 - 25 Aligned: 25 Modelled: 25 Confidence: 20.4% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:sarcolipin; PDBTitle: nmr structure of sarcolipin Phyre2 PDB 1ar1 chain B Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 17.0% Identity: 4% PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment Phyre2 PDB 1qle chain B Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 17.0% Identity: 4% PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment Phyre2 PDB 2kk7 chain A Region: 62 - 96 Aligned: 35 Modelled: 35 Confidence: 16.5% Identity: 46% PDB header:hydrolase Chain: A: PDB Molecule:v-type atp synthase subunit e; PDBTitle: nmr solution structure of the n terminal domain of subunit e2 (e1-52) of a1ao atp synthase from methanocaldococcus3 jannaschii Phyre2 PDB 3ehb chain B domain 2 Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 14.6% Identity: 4% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1fft chain B domain 2 Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 12.7% Identity: 12% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 1 c1b9uA_ 2 d1l2pa_ 3 c3k5bE_ 4 d2oara1 5 c2oarA_ 6 c2khkA_ 7 c3hzqA_ 8 c2rddB_ 9 c3k5bB_ 10 c1y4cA_ 11 c1qcrD_ 12 c3rfrI_ 13 c2k88A_ 14 d3dtub2 15 c1jdmA_ 16 c1ar1B_ 17 c1qleB_ 18 c2kk7A_ 19 d3ehbb2 20 d1fftb2 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

Detailed template information

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

1 c1b9uA_ 98.3 100 PDB header:hydrolase Chain: A: PDB Molecule:protein (atp synthase); PDBTitle: membrane domain of the subunit b of the e.coli atp synthase 2 d1l2pa_ 97.6 100 Fold:Single transmembrane helix Superfamily:F1F0 ATP synthase subunit B, membrane domain Family:F1F0 ATP synthase subunit B, membrane domain 3 c3k5bE_ 96.3 19 PDB header:hydrolase Chain: E: PDB Molecule:v-type atp synthase subunit e; PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase 4 d2oara1 90.9 24 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 5 c2oarA_ 90.1 16 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 6 c2khkA_ 87.9 100 PDB header:transport protein Chain: A: PDB Molecule:atp synthase subunit b; PDBTitle: nmr solution structure of the b30-82 domain of subunit b of2 escherichia coli f1fo atp synthase 7 c3hzqA_ 81.0 7 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state 8 c2rddB_ 77.0 15 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 9 c3k5bB_ 76.3 21 PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase, subunit (vapc-therm); PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase 10 c1y4cA_ 70.0 18 PDB header:de novo protein Chain: A: PDB Molecule:maltose binding protein fused with designed PDBTitle: designed helical protein fusion mbp 11 c1qcrD_ 43.6 6 PDB header: PDB COMPND: 12 c3rfrI_ 37.3 3 PDB header:oxidoreductase Chain: I: PDB Molecule:pmob; PDBTitle: crystal structure of particulate methane monooxygenase (pmmo) from2 methylocystis sp. strain m 13 c2k88A_ 33.0 34 PDB header:hydrolase Chain: A: PDB Molecule:vacuolar proton pump subunit g; PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase 14 d3dtub2 24.9 16 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 15 c1jdmA_ 20.4 16 PDB header:membrane protein Chain: A: PDB Molecule:sarcolipin; PDBTitle: nmr structure of sarcolipin 16 c1ar1B_ 17.0 4 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment 17 c1qleB_ 17.0 4 PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment 18 c2kk7A_ 16.5 46 PDB header:hydrolase Chain: A: PDB Molecule:v-type atp synthase subunit e; PDBTitle: nmr solution structure of the n terminal domain of subunit e2 (e1-52) of a1ao atp synthase from methanocaldococcus3 jannaschii 19 d3ehbb2 14.6 4 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 20 d1fftb2 12.7 12 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 21 c1bctA_ not modelled 11.5 15 PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of proteolytic fragment 163-2312 of bacterioopsin determined from nuclear magnetic3 resonance data in solution 22 c3mk7F_ not modelled 10.2 8 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 23 d1v54d_ not modelled 9.5 17 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit IV Family:Mitochondrial cytochrome c oxidase subunit IV 24 c2y69Q_ not modelled 9.3 17 PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 25 c1ei3E_ not modelled 8.9 9 PDB header: PDB COMPND: 26 c3ghgK_ not modelled 8.9 15 PDB header:blood clotting Chain: K: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of human fibrinogen 27 c1dxzA_ not modelled 8.5 28 PDB header:transmembrane protein Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: m2 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 203 structures 28 c2k59B_ not modelled 8.3 30 PDB header:transport protein Chain: B: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of the second transmembrane domain of the2 neuronal acetylcholine receptor beta 2 subunit 29 c1m57H_ not modelled 7.9 16 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 30 c1fftG_ not modelled 7.5 12 PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli 31 c2ww9B_ not modelled 7.4 16 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 32 c1kilE_ not modelled 6.2 28 PDB header:membrane protein Chain: E: PDB Molecule:complexin i snare-complex binding region; PDBTitle: three-dimensional structure of the complexin/snare complex 33 c3bz1T_ not modelled 5.4 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 34 c3prrT_ not modelled 5.4 17 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 35 c3prqT_ not modelled 5.4 17 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 36 c3bz2T_ not modelled 5.4 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 37 c1s5lT_ not modelled 5.2 16 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 38 c1s5lt_ not modelled 5.2 16 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 39 c2axtt_ not modelled 5.2 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 40 c2axtT_ not modelled 5.2 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 41 c3a0ht_ not modelled 5.2 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of i-substituted photosystem ii complex 42 c3kziT_ not modelled 5.2 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 43 d2axtt1 not modelled 5.2 17 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein T, PsbT Family:PsbT-like 44 c3a0hT_ not modelled 5.2 17 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of i-substituted photosystem ii complex 45 c3arcT_ not modelled 5.2 17 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution

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