Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	F	L	N	M	F	F	F	D	I	Y	P	Y	I	A	G	A	V	F	L	I	G	S	W	L	R	Y	D	Y	G	Q	Y	T	W	R	A	A	S	S	Q	M	L	D	R	K	G	M	N	L	A	S	N	L	F	H	I	G	I	L
Secondary structure
SS confidence
Disorder		?	?																													?	?	?													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	I	F	V	G	H	F	F	G	M	L	T	P	H	W	M	Y	E	A	W	L	P	I	E	V	K	Q	K	M	A	M	F	A	G	G	A	S	G	V	L	C	L	I	G	G	V	L	L	L	K	R	R	L	F	S	P	R	V	R	A
Secondary structure
SS confidence
Disorder																																																											?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	T	T	G	A	D	I	L	I	L	S	L	L	V	I	Q	C	A	L	G	L	L	T	I	P	F	S	A	Q	H	M	D	G	S	E	M	M	K	L	V	G	W	A	Q	S	V	V	T	F	H	G	G	A	S	Q	H	L	D	G	V
Secondary structure
SS confidence
Disorder																																																					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.
Sequence		A	F	I	F	R	L	H	L	V	L	G	M	T	L	F	L	L	F	P	F	S	R	L	I	H	I	W	S	V	P	V	E	Y	L	T	R	K	Y	Q	L	V	R	A	R	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 1y5i chain C domain 1 Region: 2 - 225 Aligned: 216 Modelled: 224 Confidence: 100.0% Identity: 100% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 2knc chain A Region: 88 - 126 Aligned: 39 Modelled: 39 Confidence: 73.6% Identity: 26% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1kqf chain C Region: 54 - 199 Aligned: 123 Modelled: 123 Confidence: 67.3% Identity: 11% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 2klu chain A Region: 89 - 122 Aligned: 34 Modelled: 34 Confidence: 58.3% Identity: 26% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 3kdp chain G Region: 86 - 112 Aligned: 27 Modelled: 27 Confidence: 55.5% Identity: 15% PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 3kdp chain H Region: 86 - 112 Aligned: 27 Modelled: 27 Confidence: 55.5% Identity: 15% PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 2k1a chain A Region: 91 - 119 Aligned: 29 Modelled: 29 Confidence: 46.6% Identity: 31% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 2jp3 chain A Region: 86 - 122 Aligned: 37 Modelled: 37 Confidence: 26.5% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 2jo1 chain A Region: 86 - 113 Aligned: 28 Modelled: 28 Confidence: 13.3% Identity: 25% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2k9y chain B Region: 82 - 112 Aligned: 31 Modelled: 31 Confidence: 9.4% Identity: 32% PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 1ar1 chain A Region: 45 - 122 Aligned: 78 Modelled: 78 Confidence: 9.1% Identity: 17% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 2zxe chain G Region: 86 - 109 Aligned: 24 Modelled: 24 Confidence: 7.1% Identity: 29% PDB header:hydrolase/transport protein Chain: G: PDB Molecule:phospholemman-like protein; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state Phyre2 PDB 2k9y chain A Region: 82 - 112 Aligned: 31 Modelled: 31 Confidence: 7.0% Identity: 32% PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 3rko chain A Region: 17 - 36 Aligned: 20 Modelled: 20 Confidence: 5.7% Identity: 25% PDB header:oxidoreductase Chain: A: PDB Molecule:nadh-quinone oxidoreductase subunit a; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2ww9 chain B Region: 187 - 214 Aligned: 25 Modelled: 28 Confidence: 5.7% Identity: 28% 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 Phyre2 PDB 1wpg chain A domain 4 Region: 15 - 115 Aligned: 94 Modelled: 101 Confidence: 5.4% Identity: 12% Fold: Calcium ATPase, transmembrane domain M Superfamily: Calcium ATPase, transmembrane domain M Family: Calcium ATPase, transmembrane domain M Phyre2 PDB 2k1k chain B Region: 86 - 112 Aligned: 27 Modelled: 27 Confidence: 5.3% Identity: 26% PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 Phyre2 PDB 2k1l chain A Region: 86 - 112 Aligned: 27 Modelled: 27 Confidence: 5.3% Identity: 26% PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 Phyre2 PDB 2k1l chain B Region: 86 - 112 Aligned: 27 Modelled: 27 Confidence: 5.3% Identity: 26% PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 Phyre2 PDB 2k1k chain A Region: 86 - 112 Aligned: 27 Modelled: 27 Confidence: 5.3% Identity: 26% PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 Phyre2 1 d1y5ic1 2 c2kncA_ 3 d1kqfc_ 4 c2kluA_ 5 c3kdpG_ 6 c3kdpH_ 7 c2k1aA_ 8 c2jp3A_ 9 c2jo1A_ 10 c2k9yB_ 11 d1ar1a_ 12 c2zxeG_ 13 c2k9yA_ 14 c3rkoA_ 15 c2ww9B_ 16 d1wpga4 17 c2k1kB_ 18 c2k1lA_ 19 c2k1lB_ 20 c2k1kA_ 21

Detailed template information

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

1 d1y5ic1 100.0 100 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 2 c2kncA_ 73.6 26 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 3 d1kqfc_ 67.3 11 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 4 c2kluA_ 58.3 26 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 5 c3kdpG_ 55.5 15 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 6 c3kdpH_ 55.5 15 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 7 c2k1aA_ 46.6 31 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 8 c2jp3A_ 26.5 19 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 9 c2jo1A_ 13.3 25 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 10 c2k9yB_ 9.4 32 PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 11 d1ar1a_ 9.1 17 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 12 c2zxeG_ 7.1 29 PDB header:hydrolase/transport protein Chain: G: PDB Molecule:phospholemman-like protein; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state 13 c2k9yA_ 7.0 32 PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 14 c3rkoA_ 5.7 25 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh-quinone oxidoreductase subunit a; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 15 c2ww9B_ 5.7 28 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 16 d1wpga4 5.4 12 Fold:Calcium ATPase, transmembrane domain M Superfamily:Calcium ATPase, transmembrane domain M Family:Calcium ATPase, transmembrane domain M 17 c2k1kB_ 5.3 26 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 18 c2k1lA_ 5.3 26 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 19 c2k1lB_ 5.3 26 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 20 c2k1kA_ 5.3 26 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 21 c3n23E_ not modelled 5.1 8 PDB header:hydrolase Chain: E: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the high affinity complex between ouabain and the2 e2p form of the sodium-potassium pump

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

---

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