Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	H	S	D	Q	G	V	Q	Y	K	S	N	K	Y	K	I	L	L	C	R	Y	E	A	M	Q	S	M	S	R	R	G	N	Y	L	D	N	S	P	M	G	R	V	F	R	R	F	K	S	K	W	L	A	K	G	G	Y	G	D	F
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		S	H	A	V	R	D	I	K	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 3f9k chain V Region: 2 - 67 Aligned: 66 Modelled: 66 Confidence: 99.4% Identity: 17% 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: 2 - 51 Aligned: 50 Modelled: 50 Confidence: 99.3% Identity: 22% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3nf9 chain A Region: 1 - 51 Aligned: 51 Modelled: 51 Confidence: 99.3% 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: 1 - 51 Aligned: 51 Modelled: 51 Confidence: 99.2% Identity: 20% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1cxq chain A Region: 2 - 51 Aligned: 46 Modelled: 50 Confidence: 98.9% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c0m chain A domain 2 Region: 1 - 51 Aligned: 51 Modelled: 51 Confidence: 98.8% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1ex4 chain A Region: 2 - 51 Aligned: 47 Modelled: 50 Confidence: 98.8% Identity: 13% 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: 2 - 67 Aligned: 57 Modelled: 66 Confidence: 98.6% Identity: 14% PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase Phyre2 PDB 1hyv chain A Region: 2 - 67 Aligned: 58 Modelled: 66 Confidence: 98.5% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3hpg chain C Region: 2 - 67 Aligned: 66 Modelled: 66 Confidence: 98.5% 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 3kks chain B Region: 2 - 67 Aligned: 66 Modelled: 66 Confidence: 98.3% Identity: 20% 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: 2 - 69 Aligned: 68 Modelled: 68 Confidence: 98.3% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 1exq chain A Region: 2 - 50 Aligned: 49 Modelled: 49 Confidence: 98.3% Identity: 10% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1bco chain A Region: 1 - 69 Aligned: 69 Modelled: 69 Confidence: 97.8% Identity: 13% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 3hos chain A Region: 1 - 69 Aligned: 68 Modelled: 69 Confidence: 97.8% Identity: 7% PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg Phyre2 PDB 3l2t chain B Region: 2 - 52 Aligned: 51 Modelled: 51 Confidence: 97.7% Identity: 18% 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 2f7t chain A Region: 1 - 69 Aligned: 67 Modelled: 69 Confidence: 97.7% Identity: 9% PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase Phyre2 PDB 1c6v chain A Region: 2 - 43 Aligned: 42 Modelled: 42 Confidence: 97.4% Identity: 19% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3f2k chain B Region: 1 - 69 Aligned: 67 Modelled: 69 Confidence: 97.3% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar; PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar Phyre2 PDB 3dlr chain A Region: 1 - 51 Aligned: 41 Modelled: 51 Confidence: 95.1% Identity: 22% PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase Phyre2 1 c3f9kV_ 2 d1asua_ 3 c3nf9A_ 4 c1c0mA_ 5 d1cxqa_ 6 d1c0ma2 7 c1ex4A_ 8 c1k6yB_ 9 d1hyva_ 10 c3hpgC_ 11 c3kksB_ 12 d1bcoa2 13 d1exqa_ 14 c1bcoA_ 15 c3hosA_ 16 c3l2tB_ 17 c2f7tA_ 18 d1c6va_ 19 c3f2kB_ 20 c3dlrA_ 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 c3f9kV_ 99.4 17 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 2 d1asua_ 99.3 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 3 c3nf9A_ 99.3 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 4 c1c0mA_ 99.2 20 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 5 d1cxqa_ 98.9 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 6 d1c0ma2 98.8 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 7 c1ex4A_ 98.8 13 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 8 c1k6yB_ 98.6 14 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 9 d1hyva_ 98.5 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 10 c3hpgC_ 98.5 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 11 c3kksB_ 98.3 20 PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii 12 d1bcoa2 98.3 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 13 d1exqa_ 98.3 10 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 14 c1bcoA_ 97.8 13 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 15 c3hosA_ 97.8 7 PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg 16 c3l2tB_ 97.7 18 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) 17 c2f7tA_ 97.7 9 PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase 18 d1c6va_ 97.4 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 19 c3f2kB_ 97.3 13 PDB header:transferase Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar; PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar 20 c3dlrA_ 95.1 22 PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase 21 c2i8bB_ not modelled 38.3 29 PDB header:viral protein Chain: B: PDB Molecule:minor nucleoprotein vp30; PDBTitle: crystal structure of the c-terminal domain of ebola virus vp30 22 d1b7ea_ not modelled 14.6 8 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 23 c1dkgB_ not modelled 14.0 6 PDB header:complex (hsp24/hsp70) Chain: B: PDB Molecule:nucleotide exchange factor grpe; PDBTitle: crystal structure of the nucleotide exchange factor grpe2 bound to the atpase domain of the molecular chaperone dnak 24 c3en9B_ not modelled 11.3 12 PDB header:hydrolase Chain: B: PDB Molecule:o-sialoglycoprotein endopeptidase/protein kinase; PDBTitle: structure of the methanococcus jannaschii kae1-bud32 fusion2 protein 25 c3lo0A_ not modelled 7.6 19 PDB header:hydrolase Chain: A: PDB Molecule:inorganic pyrophosphatase; PDBTitle: crystal structure of inorganic pyrophosphatase from2 ehrlichia chaffeensis 26 c2vkcA_ not modelled 7.5 23 PDB header:hydrolase Chain: A: PDB Molecule:nedd4-binding protein 2; PDBTitle: solution structure of the b3bp smr domain 27 c3fq3H_ not modelled 7.4 30 PDB header:hydrolase Chain: H: PDB Molecule:inorganic pyrophosphatase:bacterial/archaeal inorganic PDBTitle: crystal structure of inorganic phosphatase from brucella melitensis 28 d1i40a_ not modelled 6.6 27 Fold:OB-fold Superfamily:Inorganic pyrophosphatase Family:Inorganic pyrophosphatase 29 d2prda_ not modelled 6.5 20 Fold:OB-fold Superfamily:Inorganic pyrophosphatase Family:Inorganic pyrophosphatase 30 d1udea_ not modelled 6.4 27 Fold:OB-fold Superfamily:Inorganic pyrophosphatase Family:Inorganic pyrophosphatase 31 c3d63B_ not modelled 6.0 27 PDB header:hydrolase Chain: B: PDB Molecule:inorganic pyrophosphatase; PDBTitle: crystal structure of inorganic pyrophosphatase from burkholderia2 pseudomallei 32 d1twla_ not modelled 5.9 27 Fold:OB-fold Superfamily:Inorganic pyrophosphatase Family:Inorganic pyrophosphatase

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