Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	A	I	N	A	K	R	V	Y	R	I	M	R	Q	N	A	L	L	L	E	R	K	P	A	V	P	P	S	K	R	A	H	T	G	R	V	A	V	K	E	S	N	Q	R	W	C	S	D	G	F	E	F	C	C	D	N	G	E	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?																				?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	R	V	T	F	A	L	D	C	C	D	R	E	A	L	H	W	A	V	T	T	G	G	F	N	S	E	T	V	Q	D	V	M	L	G	A	V	E	R	R	F	G	N	D	L	P	S	S	P	V	E	W	L	T	D	N	G	S	C	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	A	N	E	T	R	Q	F	A	R	M	L	G	L	E	P	K	N	T	A	V	R	S	P	E	S	N	G	I	A	E	S	F	V	K	T	I	K	R	D	Y	I	S	I	M	P	K	P	D	G	L	T	A	A	K	N	L	A	E	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.
Sequence		F	E	H	Y	N	E	W	H	P	H	S	A	L	G	Y	R	S	P	R	E	Y	L	R	Q	R	A	C	N	G	L	S	D	N	R	C	L	E	I
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: 39 - 202 Aligned: 147 Modelled: 164 Confidence: 99.8% Identity: 18% 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: 35 - 202 Aligned: 157 Modelled: 161 Confidence: 99.8% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c0m chain A Region: 36 - 212 Aligned: 166 Modelled: 177 Confidence: 99.8% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1bco chain A domain 2 Region: 41 - 204 Aligned: 159 Modelled: 164 Confidence: 99.8% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 1asu chain A Region: 35 - 198 Aligned: 153 Modelled: 164 Confidence: 99.8% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1exq chain A Region: 40 - 211 Aligned: 147 Modelled: 171 Confidence: 99.8% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3nf9 chain A Region: 41 - 203 Aligned: 145 Modelled: 163 Confidence: 99.7% 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 1ex4 chain A Region: 40 - 204 Aligned: 144 Modelled: 164 Confidence: 99.7% Identity: 18% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain Phyre2 PDB 1bco chain A Region: 38 - 204 Aligned: 161 Modelled: 167 Confidence: 99.7% Identity: 16% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 3kks chain B Region: 44 - 211 Aligned: 150 Modelled: 168 Confidence: 99.7% Identity: 15% 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 1c6v chain A Region: 45 - 202 Aligned: 130 Modelled: 158 Confidence: 99.7% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1cxq chain A Region: 41 - 186 Aligned: 133 Modelled: 146 Confidence: 99.7% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1k6y chain B Region: 38 - 202 Aligned: 139 Modelled: 156 Confidence: 99.7% Identity: 19% 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: 42 - 211 Aligned: 141 Modelled: 170 Confidence: 99.6% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3hpg chain C Region: 40 - 208 Aligned: 151 Modelled: 169 Confidence: 99.6% Identity: 18% 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: 38 - 207 Aligned: 158 Modelled: 170 Confidence: 99.6% Identity: 12% 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 3dlr chain A Region: 40 - 206 Aligned: 145 Modelled: 167 Confidence: 99.4% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase Phyre2 PDB 3hos chain A Region: 4 - 182 Aligned: 175 Modelled: 179 Confidence: 98.7% Identity: 17% 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 2f7t chain A Region: 43 - 182 Aligned: 139 Modelled: 140 Confidence: 97.4% Identity: 15% PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase Phyre2 PDB 3f2k chain B Region: 107 - 182 Aligned: 75 Modelled: 76 Confidence: 95.6% Identity: 20% 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 1 c3f9kV_ 2 d1c0ma2 3 c1c0mA_ 4 d1bcoa2 5 d1asua_ 6 d1exqa_ 7 c3nf9A_ 8 c1ex4A_ 9 c1bcoA_ 10 c3kksB_ 11 d1c6va_ 12 d1cxqa_ 13 c1k6yB_ 14 d1hyva_ 15 c3hpgC_ 16 c3l2tB_ 17 c3dlrA_ 18 c3hosA_ 19 c2f7tA_ 20 c3f2kB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

Detailed template information

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

1 c3f9kV_ 99.8 18 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 2 d1c0ma2 99.8 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 3 c1c0mA_ 99.8 15 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 4 d1bcoa2 99.8 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 5 d1asua_ 99.8 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 6 d1exqa_ 99.8 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 7 c3nf9A_ 99.7 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 c1ex4A_ 99.7 18 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 9 c1bcoA_ 99.7 16 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 10 c3kksB_ 99.7 15 PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii 11 d1c6va_ 99.7 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 12 d1cxqa_ 99.7 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 13 c1k6yB_ 99.7 19 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 14 d1hyva_ 99.6 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 15 c3hpgC_ 99.6 18 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 16 c3l2tB_ 99.6 12 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 c3dlrA_ 99.4 12 PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase 18 c3hosA_ 98.7 17 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 19 c2f7tA_ 97.4 15 PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase 20 c3f2kB_ 95.6 20 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 21 c3mwmA_ not modelled 44.9 25 PDB header:transcription Chain: A: PDB Molecule:putative metal uptake regulation protein; PDBTitle: graded expression of zinc-responsive genes through two regulatory2 zinc-binding sites in zur 22 d1mzba_ not modelled 43.2 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FUR-like 23 c2fe3B_ not modelled 41.5 30 PDB header:dna binding protein Chain: B: PDB Molecule:peroxide operon regulator; PDBTitle: the crystal structure of bacillus subtilis perr-zn reveals a novel2 zn(cys)4 structural redox switch 24 c2o03A_ not modelled 38.0 27 PDB header:gene regulation Chain: A: PDB Molecule:probable zinc uptake regulation protein furb; PDBTitle: crystal structure of furb from m. tuberculosis- a zinc uptake2 regulator 25 c2fu4B_ not modelled 36.5 29 PDB header:dna binding protein Chain: B: PDB Molecule:ferric uptake regulation protein; PDBTitle: crystal structure of the dna binding domain of e.coli fur (ferric2 uptake regulator) 26 c2w57A_ not modelled 36.3 33 PDB header:metal transport Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: crystal structure of the vibrio cholerae ferric uptake2 regulator (fur) reveals structural rearrangement of the3 dna-binding domains 27 c2xigA_ not modelled 34.2 27 PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites 28 c3e7lD_ not modelled 34.0 17 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 29 c3eyyA_ not modelled 33.3 31 PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition 30 c2kkmA_ not modelled 28.5 15 PDB header:translation Chain: A: PDB Molecule:translation machinery-associated protein 16; PDBTitle: solution nmr structure of yeast protein yor252w [residues2 38-178]: northeast structural genomics consortium target3 yt654 31 d2aq0a1 not modelled 21.4 35 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 32 d1f1ea_ not modelled 19.4 20 Fold:Histone-fold Superfamily:Histone-fold Family:Archaeal histone 33 c1htrP_ not modelled 12.4 26 PDB header:aspartyl protease Chain: P: PDB Molecule:progastricsin (pro segment); PDBTitle: crystal and molecular structures of human progastricsin at 1.622 angstroms resolution 34 c1u78A_ not modelled 10.8 7 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 35 c1yshE_ not modelled 10.7 19 PDB header:structural protein/rna Chain: E: PDB Molecule:40s ribosomal protein s13; PDBTitle: localization and dynamic behavior of ribosomal protein l30e 36 d1gdta1 not modelled 8.6 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 37 c1s1hO_ not modelled 8.4 31 PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein s13; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. 38 c3iwfA_ not modelled 7.6 7 PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a 39 c3u5gK_ not modelled 7.6 14 PDB header:ribosome Chain: K: PDB Molecule:40s ribosomal protein s10-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution 40 c3oioA_ not modelled 7.4 47 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain- PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum 41 d1pdnc_ not modelled 6.5 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 42 d2gtad1 not modelled 6.1 4 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like

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