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	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	Y	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: 98.0% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1hyv chain A Region: 40 - 158 Aligned: 112 Modelled: 119 Confidence: 98.0% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1exq chain A Region: 40 - 159 Aligned: 114 Modelled: 120 Confidence: 97.6% Identity: 11% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1asu chain A Region: 40 - 139 Aligned: 98 Modelled: 100 Confidence: 97.4% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c0m chain A Region: 40 - 141 Aligned: 100 Modelled: 102 Confidence: 97.3% Identity: 18% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1ex4 chain A Region: 40 - 158 Aligned: 113 Modelled: 119 Confidence: 97.1% Identity: 14% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain Phyre2 PDB 3nf9 chain A Region: 40 - 159 Aligned: 114 Modelled: 120 Confidence: 96.9% 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 domain 2 Region: 40 - 141 Aligned: 100 Modelled: 102 Confidence: 96.9% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3kks chain B Region: 34 - 158 Aligned: 116 Modelled: 125 Confidence: 96.8% Identity: 21% 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 3f9k chain V Region: 40 - 158 Aligned: 113 Modelled: 119 Confidence: 96.6% Identity: 13% 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 1k6y chain B Region: 40 - 158 Aligned: 108 Modelled: 119 Confidence: 96.5% Identity: 16% PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase Phyre2 PDB 1c6v chain A Region: 35 - 158 Aligned: 118 Modelled: 124 Confidence: 96.4% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3dlr chain A Region: 40 - 140 Aligned: 100 Modelled: 101 Confidence: 93.1% Identity: 11% PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase Phyre2 PDB 3hpg chain C Region: 40 - 158 Aligned: 113 Modelled: 119 Confidence: 92.7% 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 3l2t chain B Region: 40 - 158 Aligned: 118 Modelled: 119 Confidence: 83.4% Identity: 9% 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 PDB 1bco chain A domain 2 Region: 58 - 113 Aligned: 56 Modelled: 56 Confidence: 49.1% Identity: 4% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 1bco chain A Region: 58 - 113 Aligned: 56 Modelled: 56 Confidence: 27.8% Identity: 4% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 1xb4 chain C Region: 12 - 24 Aligned: 13 Modelled: 13 Confidence: 27.0% Identity: 38% 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 Phyre2 PDB 1xb4 chain A domain 1 Region: 12 - 33 Aligned: 22 Modelled: 22 Confidence: 24.1% Identity: 41% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Vacuolar sorting protein domain Phyre2 PDB 3he5 chain D Region: 129 - 158 Aligned: 30 Modelled: 30 Confidence: 23.2% Identity: 30% PDB header:de novo protein Chain: D: PDB Molecule:synzip2; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 Phyre2 1 d1cxqa_ 2 d1hyva_ 3 d1exqa_ 4 d1asua_ 5 c1c0mA_ 6 c1ex4A_ 7 c3nf9A_ 8 d1c0ma2 9 c3kksB_ 10 c3f9kV_ 11 c1k6yB_ 12 d1c6va_ 13 c3dlrA_ 14 c3hpgC_ 15 c3l2tB_ 16 d1bcoa2 17 c1bcoA_ 18 c1xb4C_ 19 d1xb4a1 20 c3he5D_ 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 48 49 50 51 52 53 54 55

Detailed template information

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

1 d1cxqa_ 98.0 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 2 d1hyva_ 98.0 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 3 d1exqa_ 97.6 11 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 4 d1asua_ 97.4 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 5 c1c0mA_ 97.3 18 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 6 c1ex4A_ 97.1 14 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 7 c3nf9A_ 96.9 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 8 d1c0ma2 96.9 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 9 c3kksB_ 96.8 21 PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii 10 c3f9kV_ 96.6 13 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 11 c1k6yB_ 96.5 16 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 12 d1c6va_ 96.4 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 13 c3dlrA_ 93.1 11 PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase 14 c3hpgC_ 92.7 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 15 c3l2tB_ 83.4 9 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) 16 d1bcoa2 49.1 4 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 17 c1bcoA_ 27.8 4 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 18 c1xb4C_ 27.0 38 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 19 d1xb4a1 24.1 41 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 20 c3he5D_ 23.2 30 PDB header:de novo protein Chain: D: PDB Molecule:synzip2; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 21 c3cuqD_ not modelled 21.1 47 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 22 c2zmeD_ not modelled 20.6 47 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 23 d1baia_ not modelled 15.8 33 Fold:Acid proteases Superfamily:Acid proteases Family:Retroviral protease (retropepsin) 24 c2k8fB_ not modelled 14.7 29 PDB header:transferase/transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structural basis for the regulation of p53 function by p300 25 c3a2aC_ not modelled 11.6 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 26 c3e0jG_ not modelled 11.5 26 PDB header:transferase Chain: G: PDB Molecule:dna polymerase subunit delta-2; PDBTitle: x-ray structure of the complex of regulatory subunits of2 human dna polymerase delta 27 c2zkrl_ not modelled 10.8 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 28 c3bv6D_ not modelled 10.5 11 PDB header:hydrolase Chain: D: PDB Molecule:metal-dependent hydrolase; PDBTitle: crystal structure of uncharacterized metallo protein from vibrio2 cholerae with beta-lactamase like fold 29 d1sgua_ not modelled 9.8 20 Fold:Acid proteases Superfamily:Acid proteases Family:Retroviral protease (retropepsin) 30 d1v6fa_ not modelled 9.3 16 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like 31 d1az5a_ not modelled 9.3 20 Fold:Acid proteases Superfamily:Acid proteases Family:Retroviral protease (retropepsin) 32 d1nvpd2 not modelled 9.2 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 33 d1gkra1 not modelled 9.1 25 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:Hydantoinase (dihydropyrimidinase) 34 d2rspa_ not modelled 9.1 29 Fold:Acid proteases Superfamily:Acid proteases Family:Retroviral protease (retropepsin) 35 d1lyva_ not modelled 8.3 33 Fold:(Phosphotyrosine protein) phosphatases II Superfamily:(Phosphotyrosine protein) phosphatases II Family:Higher-molecular-weight phosphotyrosine protein phosphatases 36 d1hvca_ not modelled 7.4 30 Fold:Acid proteases Superfamily:Acid proteases Family:Retroviral protease (retropepsin) 37 d2jdid2 not modelled 7.0 16 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily:N-terminal domain of alpha and beta subunits of F1 ATP synthase Family:N-terminal domain of alpha and beta subunits of F1 ATP synthase 38 d2gu3a2 not modelled 7.0 16 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:PepSY-like 39 d1mabb2 not modelled 6.8 16 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily:N-terminal domain of alpha and beta subunits of F1 ATP synthase Family:N-terminal domain of alpha and beta subunits of F1 ATP synthase 40 d1nh2d2 not modelled 6.5 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 41 c2gu3A_ not modelled 6.4 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ypmb protein; PDBTitle: ypmb protein from bacillus subtilis 42 d2bg1a1 not modelled 6.4 18 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 43 d1y7ea2 not modelled 6.2 12 Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases 44 c3lk3T_ not modelled 6.1 38 PDB header:protein binding Chain: T: PDB Molecule:leucine-rich repeat-containing protein 16a; PDBTitle: crystal structure of capz bound to the cpi and csi uncapping2 motifs from carmil 45 d3c7bb2 not modelled 5.9 36 Fold:Ferredoxin-like Superfamily:Nitrite/Sulfite reductase N-terminal domain-like Family:DsrA/DsrB N-terminal-domain-like 46 d2c5wb1 not modelled 5.8 18 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 47 c2j8oA_ not modelled 5.8 11 PDB header:structural protein Chain: A: PDB Molecule:titin; PDBTitle: structure of the immunoglobulin tandem repeat of titin a168-2 a169 48 c3gebC_ not modelled 5.6 18 PDB header:hydrolase Chain: C: PDB Molecule:eyes absent homolog 2; PDBTitle: crystal structure of edeya2 49 c1tiiC_ not modelled 5.5 44 PDB header:enterotoxin Chain: C: PDB Molecule:heat labile enterotoxin type iib; PDBTitle: escherichia coli heat labile enterotoxin type iib 50 d1nfga1 not modelled 5.5 30 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:Hydantoinase (dihydropyrimidinase) 51 d2gycj1 not modelled 5.4 27 Fold:Ribosomal proteins L15p and L18e Superfamily:Ribosomal proteins L15p and L18e Family:Ribosomal proteins L15p and L18e 52 c3c7bE_ not modelled 5.3 40 PDB header:oxidoreductase Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit beta; PDBTitle: structure of the dissimilatory sulfite reductase from archaeoglobus2 fulgidus 53 d1flga_ not modelled 5.2 28 Fold:8-bladed beta-propeller Superfamily:Quinoprotein alcohol dehydrogenase-like Family:Quinoprotein alcohol dehydrogenase-like 54 d4fiva_ not modelled 5.2 15 Fold:Acid proteases Superfamily:Acid proteases Family:Retroviral protease (retropepsin) 55 c3t38B_ not modelled 5.1 15 PDB header:oxidoreductase Chain: B: PDB Molecule:arsenate reductase; PDBTitle: corynebacterium glutamicum thioredoxin-dependent arsenate reductase2 cg_arsc1'

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