Secondary structure and disorder prediction

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Sequence		M	V	S	R	Y	V	P	D	M	G	D	L	I	W	V	D	F	D	P	T	K	G	S	E	Q	A	G	H	R	P	A	V	V	L	S	P	F	M	Y	N	N	K	T	G	M	C	L	C	V	P	C	T	T	Q	S	K	G	Y	P	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.
Sequence		E	V	V	L	S	G	Q	E	R	D	G	V	A	L	A	D	Q	V	K	S	I	A	W	R	A	R	G	A	T	K	K	G	T	V	A	P	E	E	L	Q	L	I	K	A	K	I	N	V	L	I	G
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 1ub4 chain A Region: 2 - 111 Aligned: 103 Modelled: 110 Confidence: 100.0% Identity: 100% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: Kid/PemK Phyre2 PDB 1m1f chain A Region: 8 - 110 Aligned: 103 Modelled: 103 Confidence: 100.0% Identity: 29% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: Kid/PemK Phyre2 PDB 1ne8 chain A Region: 6 - 111 Aligned: 105 Modelled: 106 Confidence: 100.0% Identity: 25% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: Kid/PemK Phyre2 PDB 3jrz chain A Region: 9 - 110 Aligned: 95 Modelled: 102 Confidence: 95.7% Identity: 17% PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 Phyre2 PDB 3vub chain A Region: 17 - 110 Aligned: 89 Modelled: 94 Confidence: 94.9% Identity: 15% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: CcdB Phyre2 PDB 3llr chain A Region: 7 - 109 Aligned: 86 Modelled: 92 Confidence: 70.5% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:dna (cytosine-5)-methyltransferase 3a; PDBTitle: crystal structure of the pwwp domain of human dna (cytosine-5-)-2 methyltransferase 3 alpha Phyre2 PDB 2daq chain A domain 1 Region: 10 - 109 Aligned: 87 Modelled: 100 Confidence: 60.8% Identity: 11% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: PWWP domain Phyre2 PDB 2l89 chain A Region: 8 - 105 Aligned: 85 Modelled: 91 Confidence: 50.5% Identity: 19% PDB header:protein binding Chain: A: PDB Molecule:pwwp domain-containing protein 1; PDBTitle: solution structure of pdp1 pwwp domain reveals its unique binding2 sites for methylated h4k20 and dna Phyre2 PDB 1h3z chain A Region: 3 - 106 Aligned: 91 Modelled: 104 Confidence: 48.8% Identity: 10% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: PWWP domain Phyre2 PDB 2nlu chain A domain 1 Region: 8 - 105 Aligned: 79 Modelled: 98 Confidence: 43.6% Identity: 14% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: PWWP domain Phyre2 PDB 3mxu chain A Region: 10 - 52 Aligned: 38 Modelled: 43 Confidence: 31.2% Identity: 26% PDB header:oxidoreductase Chain: A: PDB Molecule:glycine cleavage system h protein; PDBTitle: crystal structure of glycine cleavage system protein h from bartonella2 henselae Phyre2 PDB 1cxq chain A Region: 8 - 55 Aligned: 42 Modelled: 48 Confidence: 27.9% Identity: 12% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1n27 chain A Region: 8 - 105 Aligned: 80 Modelled: 86 Confidence: 23.8% Identity: 15% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: PWWP domain Phyre2 PDB 2edg chain A Region: 10 - 52 Aligned: 38 Modelled: 43 Confidence: 23.5% Identity: 21% PDB header:biosynthetic protein Chain: A: PDB Molecule:glycine cleavage system h protein; PDBTitle: solution structure of the gcv_h domain from mouse glycine Phyre2 PDB 1khc chain A Region: 7 - 109 Aligned: 86 Modelled: 92 Confidence: 21.0% Identity: 15% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: PWWP domain Phyre2 PDB 2je6 chain I domain 1 Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 20.9% Identity: 27% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2h8k chain A Region: 2 - 23 Aligned: 21 Modelled: 22 Confidence: 20.5% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:sult1c3 splice variant d; PDBTitle: human sulfotranferase sult1c3 in complex with pap Phyre2 PDB 3a8j chain F Region: 10 - 34 Aligned: 24 Modelled: 25 Confidence: 20.2% Identity: 29% PDB header:transferase/transport protein Chain: F: PDB Molecule:glycine cleavage system h protein; PDBTitle: crystal structure of et-ehred complex Phyre2 PDB 2ja9 chain A domain 1 Region: 3 - 14 Aligned: 12 Modelled: 12 Confidence: 19.1% Identity: 33% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1onl chain A Region: 10 - 52 Aligned: 38 Modelled: 43 Confidence: 18.4% Identity: 24% Fold: Barrel-sandwich hybrid Superfamily: Single hybrid motif Family: Biotinyl/lipoyl-carrier proteins and domains Phyre2 1 d1ub4a_ 2 d1m1fa_ 3 d1ne8a_ 4 c3jrzA_ 5 d3vuba_ 6 c3llrA_ 7 d2daqa1 8 c2l89A_ 9 d1h3za_ 10 d2nlua1 11 c3mxuA_ 12 d1cxqa_ 13 d1n27a_ 14 c2edgA_ 15 d1khca_ 16 d2je6i1 17 c2h8kA_ 18 c3a8jF_ 19 d2ja9a1 20 d1onla_ 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 56 57

Detailed template information

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

1 d1ub4a_ 100.0 100 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Kid/PemK 2 d1m1fa_ 100.0 29 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Kid/PemK 3 d1ne8a_ 100.0 25 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Kid/PemK 4 c3jrzA_ 95.7 17 PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 5 d3vuba_ 94.9 15 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:CcdB 6 c3llrA_ 70.5 14 PDB header:transferase Chain: A: PDB Molecule:dna (cytosine-5)-methyltransferase 3a; PDBTitle: crystal structure of the pwwp domain of human dna (cytosine-5-)-2 methyltransferase 3 alpha 7 d2daqa1 60.8 11 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:PWWP domain 8 c2l89A_ 50.5 19 PDB header:protein binding Chain: A: PDB Molecule:pwwp domain-containing protein 1; PDBTitle: solution structure of pdp1 pwwp domain reveals its unique binding2 sites for methylated h4k20 and dna 9 d1h3za_ 48.8 10 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:PWWP domain 10 d2nlua1 43.6 14 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:PWWP domain 11 c3mxuA_ 31.2 26 PDB header:oxidoreductase Chain: A: PDB Molecule:glycine cleavage system h protein; PDBTitle: crystal structure of glycine cleavage system protein h from bartonella2 henselae 12 d1cxqa_ 27.9 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 13 d1n27a_ 23.8 15 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:PWWP domain 14 c2edgA_ 23.5 21 PDB header:biosynthetic protein Chain: A: PDB Molecule:glycine cleavage system h protein; PDBTitle: solution structure of the gcv_h domain from mouse glycine 15 d1khca_ 21.0 15 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:PWWP domain 16 d2je6i1 20.9 27 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 17 c2h8kA_ 20.5 29 PDB header:transferase Chain: A: PDB Molecule:sult1c3 splice variant d; PDBTitle: human sulfotranferase sult1c3 in complex with pap 18 c3a8jF_ 20.2 29 PDB header:transferase/transport protein Chain: F: PDB Molecule:glycine cleavage system h protein; PDBTitle: crystal structure of et-ehred complex 19 d2ja9a1 19.1 33 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 20 d1onla_ 18.4 24 Fold:Barrel-sandwich hybrid Superfamily:Single hybrid motif Family:Biotinyl/lipoyl-carrier proteins and domains 21 c2x35A_ not modelled 16.7 13 PDB header:transcription Chain: A: PDB Molecule:peregrin; PDBTitle: molecular basis of histone h3k36me3 recognition by the pwwp2 domain of brpf1. 22 c3pfsA_ not modelled 16.2 16 PDB header:protein binding Chain: A: PDB Molecule:bromodomain and phd finger-containing protein 3; PDBTitle: pwwp domain of human bromodomain and phd finger-containing protein 3 23 c2ja9A_ not modelled 15.7 33 PDB header:rna-binding protein Chain: A: PDB Molecule:exosome complex exonuclease rrp40; PDBTitle: structure of the n-terminal deletion of yeast exosome2 component rrp40 24 d2nn6g1 not modelled 14.4 55 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 25 c3iftA_ not modelled 14.2 21 PDB header:oxidoreductase Chain: A: PDB Molecule:glycine cleavage system h protein; PDBTitle: crystal structure of glycine cleavage system protein h from2 mycobacterium tuberculosis, using x-rays from the compact light3 source. 26 d2nn6i1 not modelled 13.8 31 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 27 d1aqua_ not modelled 13.4 21 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 28 d2ba0a1 not modelled 13.4 44 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 29 c2gfuA_ not modelled 13.0 18 PDB header:dna binding protein Chain: A: PDB Molecule:dna mismatch repair protein msh6; PDBTitle: nmr solution structure of the pwwp domain of mismatch2 repair protein hmsh6 30 d1vqoq1 not modelled 12.8 24 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:Ribosomal proteins L24p and L21e 31 d1b12a_ not modelled 12.5 14 Fold:LexA/Signal peptidase Superfamily:LexA/Signal peptidase Family:Type 1 signal peptidase 32 d1hpca_ not modelled 12.3 16 Fold:Barrel-sandwich hybrid Superfamily:Single hybrid motif Family:Biotinyl/lipoyl-carrier proteins and domains 33 d2nn6h1 not modelled 11.9 36 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 34 d3bfxa1 not modelled 11.1 19 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 35 c2jnsA_ not modelled 10.8 14 PDB header:unknown function Chain: A: PDB Molecule:bromodomain-containing protein 4; PDBTitle: solution structure of the bromodomain-containing protein 42 et domain 36 d1xv1a_ not modelled 9.8 16 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 37 c2zvpX_ not modelled 9.6 16 PDB header:transferase Chain: X: PDB Molecule:tyrosine-ester sulfotransferase; PDBTitle: crystal structure of mouse cytosolic sulfotransferase msult1d1 complex2 with pap and p-nitrophenol 38 d1q44a_ not modelled 9.3 29 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 39 d1zaka2 not modelled 9.2 23 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 40 c2ba0A_ not modelled 9.1 42 PDB header:rna binding protein Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4; PDBTitle: archaeal exosome core 41 d2z0sa1 not modelled 7.9 56 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 42 c2gwhA_ not modelled 7.6 19 PDB header:transferase Chain: A: PDB Molecule:sulfotransferase 1c2; PDBTitle: human sulfotranferase sult1c2 in complex with pap and2 pentachlorophenol 43 c2jysA_ not modelled 7.4 20 PDB header:hydrolase Chain: A: PDB Molecule:protease/reverse transcriptase; PDBTitle: solution structure of simian foamy virus (mac) protease 44 d1okja2 not modelled 7.3 22 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:YeaZ-like 45 c2ky9A_ not modelled 7.0 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ydhk; PDBTitle: solution nmr structure of ydhk c-terminal domain from b.subtilis,2 northeast structural genomics consortium target target sr518 46 d1j99a_ not modelled 6.6 26 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 47 d1ubea2 not modelled 6.4 24 Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain 48 c2nn6G_ not modelled 6.4 50 PDB header:hydrolase/transferase Chain: G: PDB Molecule:exosome complex exonuclease rrp40; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 49 d1ls6a_ not modelled 6.3 21 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 50 c3u3oA_ not modelled 6.3 21 PDB header:transferase Chain: A: PDB Molecule:sulfotransferase 1a1; PDBTitle: crystal structure of human sult1a1 bound to pap and two 3-cyano-7-2 hydroxycoumarin 51 d1mo6a2 not modelled 6.3 24 Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain 52 d1c0ma2 not modelled 6.2 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 53 c2dgyA_ not modelled 5.9 36 PDB header:translation Chain: A: PDB Molecule:mgc11102 protein; PDBTitle: solution structure of the eukaryotic initiation factor 1a2 in mgc11102 protein 54 c2zkrq_ not modelled 5.9 15 PDB header:ribosomal protein/rna Chain: Q: PDB Molecule:rna expansion segment es31 part ii; 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 55 d2a3ra1 not modelled 5.8 19 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 56 c1zd1B_ not modelled 5.7 19 PDB header:transferase Chain: B: PDB Molecule:sulfotransferase 4a1; PDBTitle: human sulfortransferase sult4a1 57 c3lyiA_ not modelled 5.6 14 PDB header:transcription Chain: A: PDB Molecule:bromodomain-containing protein 1; PDBTitle: pwwp domain of human bromodomain-containing protein 1

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