Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	G	N	S	P	H	Y	G	R	W	P	Q	H	D	F	T	S	L	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	S	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	L	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 1cxq chain A Region: 40 - 165 Aligned: 124 Modelled: 126 Confidence: 96.9% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1hyv chain A Region: 42 - 157 Aligned: 109 Modelled: 116 Confidence: 96.7% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1exq chain A Region: 42 - 157 Aligned: 110 Modelled: 116 Confidence: 96.5% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1asu chain A Region: 24 - 166 Aligned: 132 Modelled: 143 Confidence: 96.0% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1ex4 chain A Region: 42 - 157 Aligned: 105 Modelled: 116 Confidence: 94.8% Identity: 16% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain Phyre2 PDB 1c6v chain A Region: 55 - 157 Aligned: 103 Modelled: 103 Confidence: 94.2% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1k6y chain B Region: 55 - 157 Aligned: 103 Modelled: 103 Confidence: 94.2% Identity: 14% 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: 45 - 157 Aligned: 108 Modelled: 113 Confidence: 93.2% Identity: 12% 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 1c0m chain A domain 2 Region: 40 - 160 Aligned: 119 Modelled: 121 Confidence: 93.1% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3nf9 chain A Region: 38 - 157 Aligned: 114 Modelled: 120 Confidence: 92.6% Identity: 17% 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: 89.5% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 3dlr chain A Region: 39 - 160 Aligned: 119 Modelled: 122 Confidence: 88.7% Identity: 12% 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: 84.0% Identity: 10% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 1bco chain A domain 2 Region: 56 - 167 Aligned: 108 Modelled: 112 Confidence: 69.1% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 3kks chain B Region: 55 - 167 Aligned: 111 Modelled: 113 Confidence: 66.1% 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 2k8f chain B Region: 79 - 95 Aligned: 17 Modelled: 17 Confidence: 45.4% Identity: 29% 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: 36.2% Identity: 30% PDB header:de novo protein Chain: D: PDB Molecule:synzip2; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 Phyre2 PDB 3hpg chain C Region: 58 - 157 Aligned: 95 Modelled: 100 Confidence: 34.1% Identity: 15% 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 1q2i chain A Region: 79 - 93 Aligned: 15 Modelled: 15 Confidence: 20.7% Identity: 27% 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 Phyre2 PDB 3l2t chain B Region: 40 - 157 Aligned: 117 Modelled: 118 Confidence: 18.9% Identity: 8% 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 d1cxqa_ 2 d1hyva_ 3 d1exqa_ 4 d1asua_ 5 c1ex4A_ 6 d1c6va_ 7 c1k6yB_ 8 c3f9kV_ 9 d1c0ma2 10 c3nf9A_ 11 c1c0mA_ 12 c3dlrA_ 13 c1bcoA_ 14 d1bcoa2 15 c3kksB_ 16 c2k8fB_ 17 c3he5D_ 18 c3hpgC_ 19 c1q2iA_ 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 d1cxqa_ 96.9 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 2 d1hyva_ 96.7 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 3 d1exqa_ 96.5 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 4 d1asua_ 96.0 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 5 c1ex4A_ 94.8 16 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 6 d1c6va_ 94.2 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 7 c1k6yB_ 94.2 14 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 8 c3f9kV_ 93.2 12 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 9 d1c0ma2 93.1 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 10 c3nf9A_ 92.6 17 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 11 c1c0mA_ 89.5 16 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 12 c3dlrA_ 88.7 12 PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase 13 c1bcoA_ 84.0 10 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 14 d1bcoa2 69.1 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 15 c3kksB_ 66.1 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 16 c2k8fB_ 45.4 29 PDB header:transferase/transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structural basis for the regulation of p53 function by p300 17 c3he5D_ 36.2 30 PDB header:de novo protein Chain: D: PDB Molecule:synzip2; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 18 c3hpgC_ 34.1 15 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 19 c1q2iA_ 20.7 27 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 20 c3l2tB_ 18.9 8 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 d2olua2 not modelled 18.4 14 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 22 c2l14B_ not modelled 18.0 29 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 23 d1nvpd2 not modelled 16.6 38 Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain 24 d1st9a_ not modelled 16.5 25 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 25 c3dwkC_ not modelled 14.4 18 PDB header:transferase Chain: C: PDB Molecule:penicillin-binding protein 2; PDBTitle: identification of dynamic structural motifs involved in2 peptidoglycan glycosyltransfer 26 c2glfB_ not modelled 13.4 11 PDB header:hydrolase Chain: B: PDB Molecule:probable m18-family aminopeptidase 1; PDBTitle: crystal structure of aminipeptidase (m18 family) from thermotoga2 maritima 27 d1nh2d2 not modelled 12.1 25 Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain 28 c3dacB_ not modelled 10.8 36 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 29 c3dacP_ not modelled 10.7 36 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 30 c2vknA_ not modelled 10.4 4 PDB header:membrane protein Chain: A: PDB Molecule:protein ssu81; PDBTitle: yeast sho1 sh3 domain complexed with a peptide from pbs2 31 c1nvpD_ not modelled 10.3 15 PDB header:transcription/dna Chain: D: PDB Molecule:transcription initiation factor iia gamma chain; PDBTitle: human tfiia/tbp/dna complex 32 d1qnta2 not modelled 9.8 20 Fold:Ribonuclease H-like motif Superfamily:Methylated DNA-protein cysteine methyltransferase domain Family:Methylated DNA-protein cysteine methyltransferase domain 33 d1e42a2 not modelled 9.7 6 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 34 c3a2aC_ not modelled 9.5 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 35 c3bpjD_ not modelled 7.6 9 PDB header:translation Chain: D: PDB Molecule:eukaryotic translation initiation factor 3 subunit j; PDBTitle: crystal structure of human translation initiation factor 3, subunit 12 alpha 36 c3pp5A_ not modelled 7.0 19 PDB header:structural protein Chain: A: PDB Molecule:brk1; PDBTitle: high-resolution structure of the trimeric scar/wave complex precursor2 brk1 37 c2juiA_ not modelled 7.0 33 PDB header:toxin Chain: A: PDB Molecule:plne; PDBTitle: three-dimensional structure of the two peptides that2 constitute the two-peptide bacteriocin plantaracin ef 38 c3pf6C_ not modelled 6.8 29 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein pp-luz7_gp033; PDBTitle: the structure of uncharacterized protein pp-luz7_gp033 from2 pseudomonas phage luz7. 39 d1y7ea2 not modelled 6.6 11 Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases 40 d1v6fa_ not modelled 6.4 9 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like 41 d1nc7a_ not modelled 6.4 24 Fold:Hypothetical protein TM1070 Superfamily:Hypothetical protein TM1070 Family:Hypothetical protein TM1070 42 d1t1ea2 not modelled 6.1 20 Fold:Ferredoxin-like Superfamily:Protease propeptides/inhibitors Family:Subtilase propeptides/inhibitors 43 d2bg1a1 not modelled 6.1 18 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 44 c3p8cE_ not modelled 5.9 19 PDB header:protein binding Chain: E: PDB Molecule:probable protein brick1; PDBTitle: structure and control of the actin regulatory wave complex 45 c2gljR_ not modelled 5.7 11 PDB header:hydrolase Chain: R: PDB Molecule: PDBTitle: crystal structure of aminopeptidase i from clostridium2 acetobutylicum 46 d1ce7b2 not modelled 5.5 31 Fold:beta-Trefoil Superfamily:Ricin B-like lectins Family:Ricin B-like 47 d2je8a2 not modelled 5.4 21 Fold:Immunoglobulin-like beta-sandwich Superfamily:beta-Galactosidase/glucuronidase domain Family:beta-Galactosidase/glucuronidase 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

---

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