Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	S	K	M	I	V	R	T	K	F	I	D	R	A	C	H	W	T	V	V	I	C	F	F	L	V	A	L	S	G	I	S	F	F	F	P	T	L	Q	W	L	T	Q	T	F	G	T	P	Q	M	G	R	I	L	H	P	F	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	I	A	I	F	V	A	L	M	F	M	F	V	R	F	V	H	H	N	I	P	D	K	K	D	I	P	W	L	L	N	I	V	E	V	L	K	G	N	E	H	K	V	A	D	V	G	K	Y	N	A	G	Q	K	M	M	F	W	S	I
Secondary structure
SS confidence
Disorder																			?																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	S	M	I	F	V	L	L	V	T	G	V	I	I	W	R	P	Y	F	A	Q	Y	F	P	M	Q	V	V	R	Y	S	L	L	I	H	A	A	A	G	I	I	L	I	H	A	I	L	I	H	M	Y	M	A	F	W	V	K	G	S	I
Secondary structure
SS confidence
Disorder																				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.
Sequence		K	G	M	I	E	G	K	V	S	R	R	W	A	K	K	H	H	P	R	W	Y	R	E	I	E	K	A	E	A	K	K	E	S	E	E	G	I
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 1kqf chain C Region: 2 - 217 Aligned: 216 Modelled: 216 Confidence: 100.0% Identity: 100% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 3cx5 chain C domain 2 Region: 20 - 173 Aligned: 153 Modelled: 152 Confidence: 97.8% Identity: 12% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2qjk chain M Region: 20 - 174 Aligned: 154 Modelled: 155 Confidence: 97.7% Identity: 14% PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin Phyre2 PDB 1q90 chain B Region: 20 - 173 Aligned: 153 Modelled: 154 Confidence: 97.6% Identity: 11% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2e74 chain A domain 1 Region: 20 - 173 Aligned: 153 Modelled: 153 Confidence: 97.6% Identity: 14% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3cx5 chain N Region: 20 - 189 Aligned: 169 Modelled: 170 Confidence: 97.5% Identity: 13% PDB header:oxidoreductase Chain: N: PDB Molecule:cytochrome b; PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer. Phyre2 PDB 1ppj chain C domain 2 Region: 20 - 173 Aligned: 151 Modelled: 154 Confidence: 97.4% Identity: 16% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1bcc chain C domain 3 Region: 20 - 173 Aligned: 151 Modelled: 154 Confidence: 97.4% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3cwb chain C Region: 20 - 179 Aligned: 157 Modelled: 160 Confidence: 97.3% Identity: 13% PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d Phyre2 PDB 1y5i chain C domain 1 Region: 16 - 166 Aligned: 114 Modelled: 123 Confidence: 38.1% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 2kyg chain C Region: 185 - 207 Aligned: 22 Modelled: 23 Confidence: 16.4% Identity: 23% PDB header:protein binding Chain: C: PDB Molecule:protein cbfa2t1; PDBTitle: structure of the aml1-eto nervy domain - pka(riia) complex and its2 contribution to aml1-eto activity Phyre2 PDB 2lev chain A Region: 198 - 212 Aligned: 15 Modelled: 15 Confidence: 13.3% Identity: 47% PDB header:transcription regulator/dna Chain: A: PDB Molecule:ler; PDBTitle: structure of the dna complex of the c-terminal domain of ler Phyre2 PDB 1ecf chain A domain 1 Region: 184 - 215 Aligned: 32 Modelled: 32 Confidence: 11.1% Identity: 9% Fold: PRTase-like Superfamily: PRTase-like Family: Phosphoribosyltransferases (PRTases) Phyre2 PDB 1fcu chain A Region: 189 - 212 Aligned: 24 Modelled: 24 Confidence: 8.2% Identity: 29% PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase Phyre2 PDB 1ecj chain B Region: 184 - 215 Aligned: 32 Modelled: 32 Confidence: 7.8% Identity: 9% PDB header:transferase Chain: B: PDB Molecule:glutamine phosphoribosylpyrophosphate PDBTitle: escherichia coli glutamine phosphoribosylpyrophosphate2 (prpp) amidotransferase complexed with 2 amp per tetramer Phyre2 PDB 2xzn chain 2 Region: 165 - 209 Aligned: 42 Modelled: 45 Confidence: 7.7% Identity: 10% PDB header:ribosome Chain: 2: PDB Molecule:40s ribosomal protein s8; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 Phyre2 PDB 1fcq chain A Region: 189 - 212 Aligned: 24 Modelled: 24 Confidence: 7.6% Identity: 29% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Bee venom hyaluronidase Phyre2 PDB 2pe4 chain A Region: 189 - 212 Aligned: 24 Modelled: 24 Confidence: 6.3% Identity: 29% PDB header:hydrolase Chain: A: PDB Molecule:hyaluronidase-1; PDBTitle: structure of human hyaluronidase 1, a hyaluronan hydrolyzing enzyme2 involved in tumor growth and angiogenesis Phyre2 PDB 3nrt chain C Region: 190 - 208 Aligned: 19 Modelled: 19 Confidence: 6.0% Identity: 21% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative ryanodine receptor; PDBTitle: the crystal strucutre of putative ryanodine receptor from bacteroides2 thetaiotaomicron vpi-5482 Phyre2 PDB 1m56 chain D Region: 1 - 34 Aligned: 34 Modelled: 34 Confidence: 5.8% Identity: 12% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 1 d1kqfc_ 2 d3cx5c2 3 c2qjkM_ 4 d1q90b_ 5 d2e74a1 6 c3cx5N_ 7 d1ppjc2 8 d1bccc3 9 c3cwbC_ 10 d1y5ic1 11 c2kygC_ 12 c2levA_ 13 d1ecfa1 14 c1fcuA_ 15 c1ecjB_ 16 c2xzn2_ 17 d1fcqa_ 18 c2pe4A_ 19 c3nrtC_ 20 d1m56d_ 21 22 23 24 25 26

Detailed template information

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

1 d1kqfc_ 100.0 100 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 2 d3cx5c2 97.8 12 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 3 c2qjkM_ 97.7 14 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 4 d1q90b_ 97.6 11 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 5 d2e74a1 97.6 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 6 c3cx5N_ 97.5 13 PDB header:oxidoreductase Chain: N: PDB Molecule:cytochrome b; PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer. 7 d1ppjc2 97.4 16 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 8 d1bccc3 97.4 15 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 c3cwbC_ 97.3 13 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 10 d1y5ic1 38.1 15 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 11 c2kygC_ 16.4 23 PDB header:protein binding Chain: C: PDB Molecule:protein cbfa2t1; PDBTitle: structure of the aml1-eto nervy domain - pka(riia) complex and its2 contribution to aml1-eto activity 12 c2levA_ 13.3 47 PDB header:transcription regulator/dna Chain: A: PDB Molecule:ler; PDBTitle: structure of the dna complex of the c-terminal domain of ler 13 d1ecfa1 11.1 9 Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases) 14 c1fcuA_ 8.2 29 PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase 15 c1ecjB_ 7.8 9 PDB header:transferase Chain: B: PDB Molecule:glutamine phosphoribosylpyrophosphate PDBTitle: escherichia coli glutamine phosphoribosylpyrophosphate2 (prpp) amidotransferase complexed with 2 amp per tetramer 16 c2xzn2_ 7.7 10 PDB header:ribosome Chain: 2: PDB Molecule:40s ribosomal protein s8; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 17 d1fcqa_ 7.6 29 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Bee venom hyaluronidase 18 c2pe4A_ 6.3 29 PDB header:hydrolase Chain: A: PDB Molecule:hyaluronidase-1; PDBTitle: structure of human hyaluronidase 1, a hyaluronan hydrolyzing enzyme2 involved in tumor growth and angiogenesis 19 c3nrtC_ 6.0 21 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative ryanodine receptor; PDBTitle: the crystal strucutre of putative ryanodine receptor from bacteroides2 thetaiotaomicron vpi-5482 20 d1m56d_ 5.8 12 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 21 c2qfaC_ not modelled 5.7 38 PDB header:cell cycle/cell cycle/cell cycle Chain: C: PDB Molecule:inner centromere protein; PDBTitle: crystal structure of a survivin-borealin-incenp core complex 22 c1v0dA_ not modelled 5.4 21 PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) 23 d1v0da_ not modelled 5.4 21 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Caspase-activated DNase, CAD (DffB, DFF40) 24 d2ct5a1 not modelled 5.4 26 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:BED zinc finger 25 c1rrzA_ not modelled 5.3 20 PDB header:structural genomics,biosynthetic protein Chain: A: PDB Molecule:glycogen synthesis protein glgs; PDBTitle: solution structure of glgs protein from e. coli 26 d1rrza_ not modelled 5.3 20 Fold:Spectrin repeat-like Superfamily:Glycogen synthesis protein GlgS Family:Glycogen synthesis protein GlgS

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