Secondary structure and disorder prediction

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Sequence		M	L	P	Q	H	S	D	I	E	I	A	W	Y	A	S	I	Q	Q	E	P	N	G	W	K	T	V	T	T	Q	F	Y	I	Q	E	F	S	E	Y	I	A	P	L	Q	D	A	V	D	L	E	I	A	T	E	E	E	R	S	L	L	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?												?			?	?	?			?																												?				?	?	?
Disorder confidence
		.
Sequence		A
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 1gk6 chain B Region: 41 - 61 Aligned: 19 Modelled: 21 Confidence: 30.6% Identity: 53% PDB header:vimentin Chain: B: PDB Molecule:vimentin; PDBTitle: human vimentin coil 2b fragment linked to gcn4 leucine2 zipper (z2b) Phyre2 PDB 2xv5 chain A Region: 41 - 61 Aligned: 19 Modelled: 21 Confidence: 28.8% Identity: 42% PDB header:structural protein Chain: A: PDB Molecule:lamin-a/c; PDBTitle: human lamin a coil 2b fragment Phyre2 PDB 2p2c chain D Region: 2 - 39 Aligned: 37 Modelled: 38 Confidence: 21.7% Identity: 24% PDB header:hydrolase Chain: D: PDB Molecule:caspase-2; PDBTitle: inhibition of caspase-2 by a designed ankyrin repeat2 protein (darpin) Phyre2 PDB 3sip chain B Region: 2 - 39 Aligned: 37 Modelled: 38 Confidence: 21.4% Identity: 22% PDB header:hydrolase/ligase/hydrolase Chain: B: PDB Molecule:caspase; PDBTitle: crystal structure of drice and diap1-bir1 complex Phyre2 PDB 3mov chain B Region: 42 - 61 Aligned: 18 Modelled: 20 Confidence: 21.1% Identity: 44% PDB header:structural protein Chain: B: PDB Molecule:lamin-b1; PDBTitle: crystal structure of human lamin-b1 coil 2 segment Phyre2 PDB 2qlj chain B Region: 2 - 37 Aligned: 35 Modelled: 36 Confidence: 20.1% Identity: 14% PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-7; PDBTitle: crystal structure of caspase-7 with inhibitor ac-wehd-cho Phyre2 PDB 1gk4 chain A Region: 42 - 61 Aligned: 18 Modelled: 20 Confidence: 16.5% Identity: 56% PDB header:vimentin Chain: A: PDB Molecule:vimentin; PDBTitle: human vimentin coil 2b fragment (cys2) Phyre2 PDB 2c1e chain B Region: 2 - 37 Aligned: 35 Modelled: 36 Confidence: 16.2% Identity: 17% PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-3 subunit p12; PDBTitle: crystal structures of caspase-3 in complex with aza-peptide michael2 acceptor inhibitors. Phyre2 PDB 2c2z chain B Region: 2 - 39 Aligned: 37 Modelled: 38 Confidence: 14.3% Identity: 16% PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-8 p10 subunit; PDBTitle: crystal structure of caspase-8 in complex with aza-peptide michael2 acceptor inhibitor Phyre2 PDB 2byk chain B Region: 21 - 47 Aligned: 27 Modelled: 27 Confidence: 14.3% Identity: 26% PDB header:dna-binding protein Chain: B: PDB Molecule:chrac-14; PDBTitle: histone fold heterodimer of the chromatin accessibility2 complex Phyre2 PDB 2byk chain B domain 1 Region: 21 - 47 Aligned: 27 Modelled: 27 Confidence: 14.3% Identity: 26% Fold: Histone-fold Superfamily: Histone-fold Family: TBP-associated factors, TAFs Phyre2 PDB 1jfi chain B Region: 21 - 47 Aligned: 27 Modelled: 27 Confidence: 14.1% Identity: 22% PDB header:transcription/dna Chain: B: PDB Molecule:transcription regulator nc2 beta chain; PDBTitle: crystal structure of the nc2-tbp-dna ternary complex Phyre2 PDB 1jfi chain B Region: 21 - 47 Aligned: 27 Modelled: 27 Confidence: 14.1% Identity: 22% Fold: Histone-fold Superfamily: Histone-fold Family: TBP-associated factors, TAFs Phyre2 PDB 1b0n chain A domain 1 Region: 36 - 60 Aligned: 25 Modelled: 25 Confidence: 13.0% Identity: 24% Fold: Dimerisation interlock Superfamily: SinR repressor dimerisation domain-like Family: SinR repressor dimerisation domain-like Phyre2 PDB 1kx5 chain B Region: 9 - 42 Aligned: 34 Modelled: 34 Confidence: 11.2% Identity: 21% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 1x8y chain A Region: 42 - 61 Aligned: 18 Modelled: 20 Confidence: 9.5% Identity: 44% PDB header:structural protein Chain: A: PDB Molecule:lamin a/c; PDBTitle: human lamin coil 2b Phyre2 PDB 1id3 chain B Region: 21 - 42 Aligned: 22 Modelled: 22 Confidence: 8.6% Identity: 23% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 1a7w chain A Region: 21 - 39 Aligned: 19 Modelled: 19 Confidence: 8.3% Identity: 16% Fold: Histone-fold Superfamily: Histone-fold Family: Archaeal histone Phyre2 PDB 3ady chain A Region: 4 - 24 Aligned: 21 Modelled: 21 Confidence: 8.3% Identity: 29% PDB header:proton transport Chain: A: PDB Molecule:dotd; PDBTitle: crystal structure of dotd from legionella Phyre2 PDB 1n1j chain A Region: 21 - 56 Aligned: 35 Modelled: 36 Confidence: 7.8% Identity: 14% Fold: Histone-fold Superfamily: Histone-fold Family: TBP-associated factors, TAFs Phyre2 1 c1gk6B_ 2 c2xv5A_ 3 c2p2cD_ 4 c3sipB_ 5 c3movB_ 6 c2qljB_ 7 c1gk4A_ 8 c2c1eB_ 9 c2c2zB_ 10 c2bykB_ 11 d2bykb1 12 c1jfiB_ 13 d1jfib_ 14 d1b0na1 15 d1kx5b_ 16 c1x8yA_ 17 d1id3b_ 18 d1a7wa_ 19 c3adyA_ 20 d1n1ja_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 c1gk6B_ 30.6 53 PDB header:vimentin Chain: B: PDB Molecule:vimentin; PDBTitle: human vimentin coil 2b fragment linked to gcn4 leucine2 zipper (z2b) 2 c2xv5A_ 28.8 42 PDB header:structural protein Chain: A: PDB Molecule:lamin-a/c; PDBTitle: human lamin a coil 2b fragment 3 c2p2cD_ 21.7 24 PDB header:hydrolase Chain: D: PDB Molecule:caspase-2; PDBTitle: inhibition of caspase-2 by a designed ankyrin repeat2 protein (darpin) 4 c3sipB_ 21.4 22 PDB header:hydrolase/ligase/hydrolase Chain: B: PDB Molecule:caspase; PDBTitle: crystal structure of drice and diap1-bir1 complex 5 c3movB_ 21.1 44 PDB header:structural protein Chain: B: PDB Molecule:lamin-b1; PDBTitle: crystal structure of human lamin-b1 coil 2 segment 6 c2qljB_ 20.1 14 PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-7; PDBTitle: crystal structure of caspase-7 with inhibitor ac-wehd-cho 7 c1gk4A_ 16.5 56 PDB header:vimentin Chain: A: PDB Molecule:vimentin; PDBTitle: human vimentin coil 2b fragment (cys2) 8 c2c1eB_ 16.2 17 PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-3 subunit p12; PDBTitle: crystal structures of caspase-3 in complex with aza-peptide michael2 acceptor inhibitors. 9 c2c2zB_ 14.3 16 PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-8 p10 subunit; PDBTitle: crystal structure of caspase-8 in complex with aza-peptide michael2 acceptor inhibitor 10 c2bykB_ 14.3 26 PDB header:dna-binding protein Chain: B: PDB Molecule:chrac-14; PDBTitle: histone fold heterodimer of the chromatin accessibility2 complex 11 d2bykb1 14.3 26 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 12 c1jfiB_ 14.1 22 PDB header:transcription/dna Chain: B: PDB Molecule:transcription regulator nc2 beta chain; PDBTitle: crystal structure of the nc2-tbp-dna ternary complex 13 d1jfib_ 14.1 22 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 14 d1b0na1 13.0 24 Fold:Dimerisation interlock Superfamily:SinR repressor dimerisation domain-like Family:SinR repressor dimerisation domain-like 15 d1kx5b_ 11.2 21 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 16 c1x8yA_ 9.5 44 PDB header:structural protein Chain: A: PDB Molecule:lamin a/c; PDBTitle: human lamin coil 2b 17 d1id3b_ 8.6 23 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 18 d1a7wa_ 8.3 16 Fold:Histone-fold Superfamily:Histone-fold Family:Archaeal histone 19 c3adyA_ 8.3 29 PDB header:proton transport Chain: A: PDB Molecule:dotd; PDBTitle: crystal structure of dotd from legionella 20 d1n1ja_ 7.8 14 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 21 c2h51B_ not modelled 7.7 11 PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:caspase-1; PDBTitle: crystal structure of human caspase-1 (glu390->asp and arg286->lys) in2 complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-3 propionylamino]-4-oxo-pentanoic acid (z-vad-fmk) 22 d1m72a_ not modelled 7.7 22 Fold:Caspase-like Superfamily:Caspase-like Family:Caspase catalytic domain 23 c3lyfB_ not modelled 7.7 4 PDB header:viral protein Chain: B: PDB Molecule:nucleocapsid protein; PDBTitle: crystal structure of the rift valley fever virus nucleocapsid protein 24 d2if1a_ not modelled 7.3 58 Fold:eIF1-like Superfamily:eIF1-like Family:eIF1-like 25 c2dtcB_ not modelled 7.3 18 PDB header:protein binding Chain: B: PDB Molecule:ral guanine nucleotide exchange factor ralgps1a; PDBTitle: crystal structure of ms0666 26 c2l5aA_ not modelled 7.2 19 PDB header:nuclear protein Chain: A: PDB Molecule:histone h3-like centromeric protein cse4, protein scm3, PDBTitle: structural basis for recognition of centromere specific histone h32 variant by nonhistone scm3 27 d1g4us1 not modelled 6.4 10 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 28 d1he1a_ not modelled 6.4 25 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 29 d1kqra_ not modelled 5.7 60 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:vp4 sialic acid binding domain 30 c1kriA_ not modelled 5.7 60 PDB header:viral protein Chain: A: PDB Molecule:vp4; PDBTitle: nmr solution structures of the rhesus rotavirus vp4 sialic2 acid binding domain without ligand 31 d2ysca1 not modelled 5.5 38 Fold:WW domain-like Superfamily:WW domain Family:WW 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