Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	G	N	R	P	H	Y	G	R	W	P	Q	H	D	F	P	P	F	K	K	L	R	P	Q	S	V	T	S	R	I	Q	P	G	S	D	V	I	V	C	A	E	M	D	E	Q	W	G	Y	V	G	A	K	S	R	Q	R	W	L	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	A	Y	D	R	L	R	K	T	V	V	A	H	V	F	G	E	R	T	M	A	T	L	G	R	L	M	S	L	L	S	P	F	D	V	V	I	W	M	T	D	G	W	P	L	Y	E	S	R	L	K	G	K	L	H	V	I	S	K	R
Secondary structure
SS confidence
Disorder																																																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.
Sequence		Y	T	Q	R	I	E	R	H	N	L	N	L	R	Q	H	L	A	R	L	G	R	K	S	L	S	F	S	K	S	V	E	Q	H	D	K	V	I	G	H	Y	L	N	I	K	H	Y	Q
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 1hyv chain A Region: 42 - 157 Aligned: 109 Modelled: 116 Confidence: 97.0% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1cxq chain A Region: 40 - 165 Aligned: 124 Modelled: 126 Confidence: 96.6% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1exq chain A Region: 55 - 157 Aligned: 103 Modelled: 103 Confidence: 96.2% Identity: 12% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1ex4 chain A Region: 42 - 157 Aligned: 110 Modelled: 116 Confidence: 95.0% Identity: 16% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain Phyre2 PDB 1k6y chain B Region: 55 - 157 Aligned: 98 Modelled: 98 Confidence: 95.0% Identity: 15% PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase Phyre2 PDB 3f9k chain V Region: 55 - 157 Aligned: 103 Modelled: 103 Confidence: 94.3% Identity: 14% PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd Phyre2 PDB 1asu chain A Region: 40 - 166 Aligned: 120 Modelled: 127 Confidence: 93.8% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c6v chain A Region: 55 - 157 Aligned: 103 Modelled: 103 Confidence: 93.6% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3nf9 chain A Region: 55 - 157 Aligned: 98 Modelled: 98 Confidence: 91.1% Identity: 16% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design Phyre2 PDB 1c0m chain A Region: 40 - 141 Aligned: 100 Modelled: 102 Confidence: 90.9% Identity: 18% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1c0m chain A domain 2 Region: 40 - 160 Aligned: 119 Modelled: 121 Confidence: 90.7% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3dlr chain A Region: 40 - 160 Aligned: 118 Modelled: 121 Confidence: 89.3% Identity: 11% PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase Phyre2 PDB 1bco chain A Region: 58 - 167 Aligned: 108 Modelled: 110 Confidence: 80.3% Identity: 10% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 3kks chain B Region: 55 - 167 Aligned: 111 Modelled: 113 Confidence: 69.6% Identity: 13% PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii Phyre2 PDB 1bco chain A domain 2 Region: 58 - 167 Aligned: 106 Modelled: 110 Confidence: 60.2% Identity: 11% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 3hpg chain C Region: 55 - 157 Aligned: 98 Modelled: 103 Confidence: 47.7% Identity: 14% PDB header:transferase Chain: C: PDB Molecule:integrase; PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces Phyre2 PDB 2k8f chain B Region: 77 - 95 Aligned: 19 Modelled: 19 Confidence: 42.7% Identity: 26% PDB header:transferase/transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structural basis for the regulation of p53 function by p300 Phyre2 PDB 3he5 chain D Region: 129 - 158 Aligned: 30 Modelled: 30 Confidence: 31.1% Identity: 30% PDB header:de novo protein Chain: D: PDB Molecule:synzip2; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 Phyre2 PDB 2l14 chain B Region: 77 - 95 Aligned: 19 Modelled: 19 Confidence: 17.5% Identity: 26% PDB header:protein binding Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structure of cbp nuclear coactivator binding domain in complex with2 p53 tad Phyre2 PDB 3l2t chain B Region: 52 - 157 Aligned: 102 Modelled: 106 Confidence: 13.3% Identity: 11% PDB header:recombination/dna Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir) Phyre2 1 d1hyva_ 2 d1cxqa_ 3 d1exqa_ 4 c1ex4A_ 5 c1k6yB_ 6 c3f9kV_ 7 d1asua_ 8 d1c6va_ 9 c3nf9A_ 10 c1c0mA_ 11 d1c0ma2 12 c3dlrA_ 13 c1bcoA_ 14 c3kksB_ 15 d1bcoa2 16 c3hpgC_ 17 c2k8fB_ 18 c3he5D_ 19 c2l14B_ 20 c3l2tB_ 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 46 47

Detailed template information

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

1 d1hyva_ 97.0 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 2 d1cxqa_ 96.6 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 3 d1exqa_ 96.2 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 4 c1ex4A_ 95.0 16 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 5 c1k6yB_ 95.0 15 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 6 c3f9kV_ 94.3 14 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 7 d1asua_ 93.8 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 8 d1c6va_ 93.6 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 9 c3nf9A_ 91.1 16 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design 10 c1c0mA_ 90.9 18 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 11 d1c0ma2 90.7 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 12 c3dlrA_ 89.3 11 PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase 13 c1bcoA_ 80.3 10 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 14 c3kksB_ 69.6 13 PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii 15 d1bcoa2 60.2 11 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 16 c3hpgC_ 47.7 14 PDB header:transferase Chain: C: PDB Molecule:integrase; PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces 17 c2k8fB_ 42.7 26 PDB header:transferase/transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structural basis for the regulation of p53 function by p300 18 c3he5D_ 31.1 30 PDB header:de novo protein Chain: D: PDB Molecule:synzip2; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 19 c2l14B_ 17.5 26 PDB header:protein binding Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structure of cbp nuclear coactivator binding domain in complex with2 p53 tad 20 c3l2tB_ 13.3 11 PDB header:recombination/dna Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir) 21 c1q2iA_ not modelled 13.3 21 PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells 22 c3dacB_ not modelled 9.6 33 PDB header:cell cycle Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structure of the human mdmx protein bound to the p53 tumor2 suppressor transactivation domain 23 c2glfB_ not modelled 9.5 11 PDB header:hydrolase Chain: B: PDB Molecule:probable m18-family aminopeptidase 1; PDBTitle: crystal structure of aminipeptidase (m18 family) from thermotoga2 maritima 24 c3dacP_ not modelled 9.4 33 PDB header:cell cycle Chain: P: PDB Molecule:cellular tumor antigen p53; PDBTitle: structure of the human mdmx protein bound to the p53 tumor2 suppressor transactivation domain 25 d1v6fa_ not modelled 9.4 9 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like 26 c3a2aC_ not modelled 9.3 69 PDB header:transport protein Chain: C: PDB Molecule:voltage-gated hydrogen channel 1; PDBTitle: the structure of the carboxyl-terminal domain of the human voltage-2 gated proton channel hv1 27 d1flga_ not modelled 7.8 23 Fold:8-bladed beta-propeller Superfamily:Quinoprotein alcohol dehydrogenase-like Family:Quinoprotein alcohol dehydrogenase-like 28 d1xb4a1 not modelled 7.7 43 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 29 d1e42a2 not modelled 7.4 5 Fold:Subdomain of clathrin and coatomer appendage domain Superfamily:Subdomain of clathrin and coatomer appendage domain Family:Clathrin adaptor appendage, alpha and beta chain-specific domain 30 c1xb4C_ not modelled 7.1 43 PDB header:unknown function Chain: C: PDB Molecule:hypothetical 23.6 kda protein in yuh1-ura8 PDBTitle: crystal structure of subunit vps25 of the endosomal2 trafficking complex escrt-ii 31 c2obnA_ not modelled 7.1 21 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a duf1611 family protein (ava_3511) from anabaena2 variabilis atcc 29413 at 2.30 a resolution 32 d2bg1a1 not modelled 7.0 18 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 33 d1lyva_ not modelled 6.6 22 Fold:(Phosphotyrosine protein) phosphatases II Superfamily:(Phosphotyrosine protein) phosphatases II Family:Higher-molecular-weight phosphotyrosine protein phosphatases 34 c3t38B_ not modelled 6.5 15 PDB header:oxidoreductase Chain: B: PDB Molecule:arsenate reductase; PDBTitle: corynebacterium glutamicum thioredoxin-dependent arsenate reductase2 cg_arsc1' 35 d1ce7b2 not modelled 6.4 31 Fold:beta-Trefoil Superfamily:Ricin B-like lectins Family:Ricin B-like 36 c2zmeD_ not modelled 6.2 43 PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex 37 c1o7dE_ not modelled 6.1 31 PDB header:hydrolase Chain: E: PDB Molecule:lysosomal alpha-mannosidase; PDBTitle: the structure of the bovine lysosomal a-mannosidase2 suggests a novel mechanism for low ph activation 38 d1y7ea2 not modelled 6.1 11 Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases 39 c3cuqD_ not modelled 6.0 43 PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex 40 c2zkrl_ not modelled 5.9 16 PDB header:ribosomal protein/rna Chain: L: PDB Molecule:rna expansion segment es20; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 41 d2c5wb1 not modelled 5.7 18 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 42 c3aa0C_ not modelled 5.6 63 PDB header:protein binding Chain: C: PDB Molecule:21mer peptide from leucine-rich repeat-containing protein PDBTitle: crystal structure of actin capping protein in complex with the cp-2 binding motif derived from carmil 43 c2wmyH_ not modelled 5.4 19 PDB header:hydrolase Chain: H: PDB Molecule:putative acid phosphatase wzb; PDBTitle: crystal structure of the tyrosine phosphatase wzb from2 escherichia coli k30 in complex with sulphate. 44 c3lk2T_ not modelled 5.2 63 PDB header:protein binding Chain: T: PDB Molecule:leucine-rich repeat-containing protein 16a; PDBTitle: crystal structure of capz bound to the uncapping motif from carmil 45 d1vqqa3 not modelled 5.2 18 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 46 c3pp5A_ not modelled 5.1 19 PDB header:structural protein Chain: A: PDB Molecule:brk1; PDBTitle: high-resolution structure of the trimeric scar/wave complex precursor2 brk1 47 d2olua2 not modelled 5.1 24 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase

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