Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	K	C	D	F	Y	H	I	I	V	L	S	L	N	F	P	G	Y	L	K	M	E	Y	G	S	T	K	M	E	E	R	L	S	R	S	P	G	G	K	L	A	L	W	A	F	Y	T	W	C	G	Y	F	V	W	A	M	A	R	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?																						?							?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	W	V	M	S	R	I	P	D	A	P	V	S	G	F	E	S	D	L	G	S	T	A	G	K	W	L	G	A	L	V	G	F	L	F	M	A	L	V	G	A	L	L	G	S	I	A	W	Y	T	R	P	R	P	A	R	S	R	R	Y
Secondary structure
SS confidence
Disorder											?	?	?	?	?	?	?	?	?																																				?	?	?	?	?	?	?
Disorder confidence
		.
Sequence		E
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 2knc chain A Region: 87 - 114 Aligned: 28 Modelled: 28 Confidence: 18.3% Identity: 25% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1z6n chain A domain 1 Region: 48 - 69 Aligned: 22 Modelled: 22 Confidence: 13.5% Identity: 18% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Thioltransferase Phyre2 PDB 1kqf chain B domain 2 Region: 86 - 116 Aligned: 31 Modelled: 31 Confidence: 12.1% Identity: 26% Fold: Single transmembrane helix Superfamily: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor Family: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor Phyre2 PDB 1whq chain A Region: 46 - 51 Aligned: 6 Modelled: 6 Confidence: 11.9% Identity: 67% Fold: dsRBD-like Superfamily: dsRNA-binding domain-like Family: Double-stranded RNA-binding domain (dsRBD) Phyre2 PDB 2ap8 chain A Region: 95 - 106 Aligned: 12 Modelled: 12 Confidence: 10.1% Identity: 42% PDB header:antibiotic Chain: A: PDB Molecule:bombinin h4; PDBTitle: solution structure of bombinin h4 in dpc micelles Phyre2 PDB 2es9 chain A domain 1 Region: 23 - 34 Aligned: 12 Modelled: 12 Confidence: 10.0% Identity: 50% Fold: YoaC-like Superfamily: YoaC-like Family: YoaC-like Phyre2 PDB 2ap7 chain A Region: 95 - 106 Aligned: 12 Modelled: 12 Confidence: 9.9% Identity: 42% PDB header:antibiotic Chain: A: PDB Molecule:bombinin h2; PDBTitle: solution structure of bombinin h2 in dpc micelles Phyre2 PDB 2k21 chain A Region: 68 - 118 Aligned: 47 Modelled: 51 Confidence: 9.5% Identity: 19% PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c Phyre2 PDB 2zcp chain A Region: 42 - 50 Aligned: 9 Modelled: 9 Confidence: 9.3% Identity: 56% PDB header:transferase Chain: A: PDB Molecule:dehydrosqualene synthase; PDBTitle: crystal structure of the c(30) carotenoid dehydrosqualene2 synthase from staphylococcus aureus complexed with3 farnesyl thiopyrophosphate Phyre2 PDB 3a0b chain X Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 8.9% Identity: 35% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3a0h chain X Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 8.9% Identity: 35% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0h chain X Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 8.9% Identity: 35% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0b chain X Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 8.9% Identity: 35% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3go5 chain A Region: 10 - 44 Aligned: 34 Modelled: 34 Confidence: 8.3% Identity: 24% PDB header:gene regulation Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains; PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution Phyre2 PDB 2ifq chain A domain 1 Region: 23 - 60 Aligned: 38 Modelled: 38 Confidence: 8.1% Identity: 24% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Thioltransferase Phyre2 PDB 2k1a chain A Region: 87 - 114 Aligned: 28 Modelled: 28 Confidence: 8.0% Identity: 25% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 1rhz chain B Region: 89 - 109 Aligned: 21 Modelled: 21 Confidence: 7.9% Identity: 19% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 1a8l chain A domain 2 Region: 26 - 53 Aligned: 27 Modelled: 28 Confidence: 7.8% Identity: 15% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: PDI-like Phyre2 PDB 1s5l chain X Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 7.6% Identity: 35% PDB header:photosynthesis Chain: X: PDB Molecule:photosystem ii psbx protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 2xpd chain C Region: 33 - 90 Aligned: 58 Modelled: 58 Confidence: 7.5% Identity: 21% PDB header:oxidoreductase Chain: C: PDB Molecule:thiol peroxidase; PDBTitle: reduced thiol peroxidase (tpx) from yersinia pseudotuberculosis Phyre2 1 c2kncA_ 2 d1z6na1 3 d1kqfb2 4 d1whqa_ 5 c2ap8A_ 6 d2es9a1 7 c2ap7A_ 8 c2k21A_ 9 c2zcpA_ 10 c3a0bX_ 11 c3a0hx_ 12 c3a0hX_ 13 c3a0bx_ 14 c3go5A_ 15 d2ifqa1 16 c2k1aA_ 17 d1rhzb_ 18 d1a8la2 19 c1s5lx_ 20 c2xpdC_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

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

1 c2kncA_ 18.3 25 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 d1z6na1 13.5 18 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase 3 d1kqfb2 12.1 26 Fold:Single transmembrane helix Superfamily:Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor Family:Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor 4 d1whqa_ 11.9 67 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 5 c2ap8A_ 10.1 42 PDB header:antibiotic Chain: A: PDB Molecule:bombinin h4; PDBTitle: solution structure of bombinin h4 in dpc micelles 6 d2es9a1 10.0 50 Fold:YoaC-like Superfamily:YoaC-like Family:YoaC-like 7 c2ap7A_ 9.9 42 PDB header:antibiotic Chain: A: PDB Molecule:bombinin h2; PDBTitle: solution structure of bombinin h2 in dpc micelles 8 c2k21A_ 9.5 19 PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c 9 c2zcpA_ 9.3 56 PDB header:transferase Chain: A: PDB Molecule:dehydrosqualene synthase; PDBTitle: crystal structure of the c(30) carotenoid dehydrosqualene2 synthase from staphylococcus aureus complexed with3 farnesyl thiopyrophosphate 10 c3a0bX_ 8.9 35 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex 11 c3a0hx_ 8.9 35 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex 12 c3a0hX_ 8.9 35 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex 13 c3a0bx_ 8.9 35 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex 14 c3go5A_ 8.3 24 PDB header:gene regulation Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains; PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution 15 d2ifqa1 8.1 24 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase 16 c2k1aA_ 8.0 25 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 17 d1rhzb_ 7.9 19 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 18 d1a8la2 7.8 15 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like 19 c1s5lx_ 7.6 35 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem ii psbx protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 20 c2xpdC_ 7.5 21 PDB header:oxidoreductase Chain: C: PDB Molecule:thiol peroxidase; PDBTitle: reduced thiol peroxidase (tpx) from yersinia pseudotuberculosis 21 d1j08a2 not modelled 7.2 22 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:PDI-like 22 d1t56a2 not modelled 7.1 13 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 23 d1u3em2 not modelled 7.0 59 Fold:DNA-binding domain of intron-encoded endonucleases Superfamily:DNA-binding domain of intron-encoded endonucleases Family:DNA-binding domain of intron-encoded endonucleases 24 d2pf1a2 not modelled 6.7 67 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 25 c2ww9B_ not modelled 6.6 25 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 26 c2ariA_ not modelled 6.5 45 PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41 27 d1f9ma_ not modelled 6.5 15 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase 28 d2fkla1 not modelled 6.4 50 Fold:Dodecin subunit-like Superfamily:Amyloid beta a4 protein copper binding domain (domain 2) Family:Amyloid beta a4 protein copper binding domain (domain 2) 29 d2e74d2 not modelled 5.8 46 Fold:Single transmembrane helix Superfamily:ISP transmembrane anchor Family:ISP transmembrane anchor 30 d1q90d_ not modelled 5.5 31 Fold:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 31 c2kb1A_ not modelled 5.4 12 PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa 32 d1rh5b_ not modelled 5.3 19 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 33 c3c5tB_ not modelled 5.3 50 PDB header:signaling protein/signaling protein Chain: B: PDB Molecule:exendin-4; PDBTitle: crystal structure of the ligand-bound glucagon-like peptide-1 receptor2 extracellular domain 34 c1ddxA_ not modelled 5.2 39 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (prostaglandin h2 synthase-2); PDBTitle: crystal structure of a mixture of arachidonic acid and prostaglandin2 bound to the cyclooxygenase active site of cox-2: prostaglandin3 structure 35 d1m7ta_ not modelled 5.2 18 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase

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