Secondary structure and disorder prediction

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10

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60

Sequence

M

M

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E

A

D

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N

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G

H

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D

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D

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K

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D

D

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Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

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L

Secondary structure

SS confidence

Disorder

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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 1xpj chain A Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 45.7% Identity: 27% Fold: HAD-like Superfamily: HAD-like Family: Hypothetical protein VC0232 Phyre2 PDB 1p6t chain A domain 2 Region: 18 - 52 Aligned: 35 Modelled: 35 Confidence: 37.8% Identity: 20% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1xty chain D Region: 16 - 55 Aligned: 40 Modelled: 40 Confidence: 24.1% Identity: 18% PDB header:hydrolase Chain: D: PDB Molecule:peptidyl-trna hydrolase; PDBTitle: crystal structure of sulfolobus solfataricus peptidyl-trna2 hydrolase Phyre2 PDB 1rlk chain A Region: 16 - 55 Aligned: 40 Modelled: 40 Confidence: 22.6% Identity: 28% Fold: Peptidyl-tRNA hydrolase II Superfamily: Peptidyl-tRNA hydrolase II Family: Peptidyl-tRNA hydrolase II Phyre2 PDB 1ltq chain A domain 1 Region: 19 - 56 Aligned: 38 Modelled: 38 Confidence: 19.1% Identity: 34% Fold: HAD-like Superfamily: HAD-like Family: phosphatase domain of polynucleotide kinase Phyre2 PDB 2gcf chain A Region: 14 - 48 Aligned: 35 Modelled: 35 Confidence: 16.7% Identity: 20% PDB header:hydrolase Chain: A: PDB Molecule:cation-transporting atpase pacs; PDBTitle: solution structure of the n-terminal domain of the coppper(i) atpase2 pacs in its apo form Phyre2 PDB 2zv3 chain E Region: 15 - 56 Aligned: 42 Modelled: 42 Confidence: 15.6% Identity: 19% PDB header:hydrolase Chain: E: PDB Molecule:peptidyl-trna hydrolase; PDBTitle: crystal structure of project mj0051 from methanocaldococcus2 jannaschii dsm 2661 Phyre2 PDB 3hie chain A Region: 42 - 60 Aligned: 19 Modelled: 19 Confidence: 15.2% Identity: 16% PDB header:exocytosis Chain: A: PDB Molecule:exocyst complex component sec3; PDBTitle: structure of the membrane-binding domain of the sec3 subunit2 of the exocyst complex Phyre2 PDB 2d3k chain A Region: 15 - 55 Aligned: 41 Modelled: 41 Confidence: 15.1% Identity: 22% PDB header:hydrolase Chain: A: PDB Molecule:peptidyl-trna hydrolase; PDBTitle: structural study on project id ph1539 from pyrococcus2 horikoshii ot3 Phyre2 PDB 2ofh chain X Region: 14 - 43 Aligned: 30 Modelled: 30 Confidence: 14.1% Identity: 27% PDB header:hydrolase, membrane protein Chain: X: PDB Molecule:zinc-transporting atpase; PDBTitle: solution structure of the n-terminal domain of the zinc(ii) atpase2 ziaa in its apo form Phyre2 PDB 2ldi chain A Region: 14 - 43 Aligned: 30 Modelled: 30 Confidence: 11.8% Identity: 27% PDB header:hydrolase Chain: A: PDB Molecule:zinc-transporting atpase; PDBTitle: nmr solution structure of ziaan sub mutant Phyre2 PDB 2obb chain A domain 1 Region: 19 - 49 Aligned: 31 Modelled: 31 Confidence: 11.3% Identity: 26% Fold: HAD-like Superfamily: HAD-like Family: BT0820-like Phyre2 PDB 3bwv chain B Region: 18 - 26 Aligned: 9 Modelled: 5 Confidence: 10.8% Identity: 44% PDB header:hydrolase Chain: B: PDB Molecule:putative 5'(3')-deoxyribonucleotidase; PDBTitle: crystal structure of deoxyribonucleotidase-like protein (np_764060.1)2 from staphylococcus epidermidis atcc 12228 at 1.55 a resolution Phyre2 PDB 1q7s chain A Region: 15 - 55 Aligned: 41 Modelled: 41 Confidence: 9.9% Identity: 20% Fold: Peptidyl-tRNA hydrolase II Superfamily: Peptidyl-tRNA hydrolase II Family: Peptidyl-tRNA hydrolase II Phyre2 PDB 1lng chain A Region: 15 - 37 Aligned: 22 Modelled: 23 Confidence: 9.7% Identity: 27% Fold: SRP19 Superfamily: SRP19 Family: SRP19 Phyre2 PDB 2k2p chain A Region: 14 - 41 Aligned: 27 Modelled: 28 Confidence: 9.5% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1203; PDBTitle: solution nmr structure of protein atu1203 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att10, ontario center for structural proteomics target atc1183 Phyre2 PDB 3dlu chain A Region: 14 - 37 Aligned: 23 Modelled: 24 Confidence: 9.5% Identity: 17% PDB header:rna binding protein Chain: A: PDB Molecule:signal recognition particle 19 kda protein; PDBTitle: structures of srp54 and srp19, the two proteins assembling2 the ribonucleic core of the signal recognition particle3 from the archaeon pyrococcus furiosus. Phyre2 PDB 2qif chain A domain 1 Region: 14 - 42 Aligned: 29 Modelled: 29 Confidence: 9.4% Identity: 24% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 3dxs chain X Region: 18 - 48 Aligned: 31 Modelled: 31 Confidence: 9.0% Identity: 13% PDB header:hydrolase Chain: X: PDB Molecule:copper-transporting atpase ran1; PDBTitle: crystal structure of a copper binding domain from hma7, a p-2 type atpase Phyre2 PDB 2kyz chain A Region: 14 - 47 Aligned: 32 Modelled: 34 Confidence: 8.5% Identity: 19% PDB header:metal binding protein Chain: A: PDB Molecule:heavy metal binding protein; PDBTitle: nmr structure of heavy metal binding protein tm0320 from thermotoga2 maritima Phyre2 1 d1xpja_ 2 d1p6ta2 3 c1xtyD_ 4 d1rlka_ 5 d1ltqa1 6 c2gcfA_ 7 c2zv3E_ 8 c3hieA_ 9 c2d3kA_ 10 c2ofhX_ 11 c2ldiA_ 12 d2obba1 13 c3bwvB_ 14 d1q7sa_ 15 d1lnga_ 16 c2k2pA_ 17 c3dluA_ 18 d2qifa1 19 c3dxsX_ 20 c2kyzA_ 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 d1xpja_ 45.7 27 Fold:HAD-like Superfamily:HAD-like Family:Hypothetical protein VC0232 2 d1p6ta2 37.8 20 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 3 c1xtyD_ 24.1 18 PDB header:hydrolase Chain: D: PDB Molecule:peptidyl-trna hydrolase; PDBTitle: crystal structure of sulfolobus solfataricus peptidyl-trna2 hydrolase 4 d1rlka_ 22.6 28 Fold:Peptidyl-tRNA hydrolase II Superfamily:Peptidyl-tRNA hydrolase II Family:Peptidyl-tRNA hydrolase II 5 d1ltqa1 19.1 34 Fold:HAD-like Superfamily:HAD-like Family:phosphatase domain of polynucleotide kinase 6 c2gcfA_ 16.7 20 PDB header:hydrolase Chain: A: PDB Molecule:cation-transporting atpase pacs; PDBTitle: solution structure of the n-terminal domain of the coppper(i) atpase2 pacs in its apo form 7 c2zv3E_ 15.6 19 PDB header:hydrolase Chain: E: PDB Molecule:peptidyl-trna hydrolase; PDBTitle: crystal structure of project mj0051 from methanocaldococcus2 jannaschii dsm 2661 8 c3hieA_ 15.2 16 PDB header:exocytosis Chain: A: PDB Molecule:exocyst complex component sec3; PDBTitle: structure of the membrane-binding domain of the sec3 subunit2 of the exocyst complex 9 c2d3kA_ 15.1 22 PDB header:hydrolase Chain: A: PDB Molecule:peptidyl-trna hydrolase; PDBTitle: structural study on project id ph1539 from pyrococcus2 horikoshii ot3 10 c2ofhX_ 14.1 27 PDB header:hydrolase, membrane protein Chain: X: PDB Molecule:zinc-transporting atpase; PDBTitle: solution structure of the n-terminal domain of the zinc(ii) atpase2 ziaa in its apo form 11 c2ldiA_ 11.8 27 PDB header:hydrolase Chain: A: PDB Molecule:zinc-transporting atpase; PDBTitle: nmr solution structure of ziaan sub mutant 12 d2obba1 11.3 26 Fold:HAD-like Superfamily:HAD-like Family:BT0820-like 13 c3bwvB_ 10.8 44 PDB header:hydrolase Chain: B: PDB Molecule:putative 5'(3')-deoxyribonucleotidase; PDBTitle: crystal structure of deoxyribonucleotidase-like protein (np_764060.1)2 from staphylococcus epidermidis atcc 12228 at 1.55 a resolution 14 d1q7sa_ 9.9 20 Fold:Peptidyl-tRNA hydrolase II Superfamily:Peptidyl-tRNA hydrolase II Family:Peptidyl-tRNA hydrolase II 15 d1lnga_ 9.7 27 Fold:SRP19 Superfamily:SRP19 Family:SRP19 16 c2k2pA_ 9.5 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1203; PDBTitle: solution nmr structure of protein atu1203 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att10, ontario center for structural proteomics target atc1183 17 c3dluA_ 9.5 17 PDB header:rna binding protein Chain: A: PDB Molecule:signal recognition particle 19 kda protein; PDBTitle: structures of srp54 and srp19, the two proteins assembling2 the ribonucleic core of the signal recognition particle3 from the archaeon pyrococcus furiosus. 18 d2qifa1 9.4 24 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 19 c3dxsX_ 9.0 13 PDB header:hydrolase Chain: X: PDB Molecule:copper-transporting atpase ran1; PDBTitle: crystal structure of a copper binding domain from hma7, a p-2 type atpase 20 c2kyzA_ 8.5 19 PDB header:metal binding protein Chain: A: PDB Molecule:heavy metal binding protein; PDBTitle: nmr structure of heavy metal binding protein tm0320 from thermotoga2 maritima 21 c2ejbA_ not modelled 8.4 30 PDB header:lyase Chain: A: PDB Molecule:probable aromatic acid decarboxylase; PDBTitle: crystal structure of phenylacrylic acid decarboxylase from2 aquifex aeolicus 22 d3erja1 not modelled 8.1 20 Fold:Peptidyl-tRNA hydrolase II Superfamily:Peptidyl-tRNA hydrolase II Family:Peptidyl-tRNA hydrolase II 23 c3s88I_ not modelled 8.0 33 PDB header:immune system/viral protein Chain: I: PDB Molecule:envelope glycoprotein; PDBTitle: crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound2 to 16f6 24 d1dosa_ not modelled 7.8 30 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class II FBP aldolase 25 c2l3mA_ not modelled 7.5 15 PDB header:metal binding protein Chain: A: PDB Molecule:copper-ion-binding protein; PDBTitle: solution structure of the putative copper-ion-binding protein from2 bacillus anthracis str. ames 26 d2f06a2 not modelled 7.5 21 Fold:Ferredoxin-like Superfamily:ACT-like Family:BT0572-like 27 d1l3ac_ not modelled 7.2 23 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:Plant transcriptional regulator PBF-2 28 d1wija_ not modelled 7.1 29 Fold:LEM/SAP HeH motif Superfamily:DNA-binding domain of EIN3-like Family:DNA-binding domain of EIN3-like 29 c3q87B_ not modelled 7.1 22 PDB header:transferase activator/transferase Chain: B: PDB Molecule:n6 adenine specific dna methylase; PDBTitle: structure of eukaryotic translation termination complex2 methyltransferase mtq2-trm112 30 c3csyK_ not modelled 6.9 38 PDB header:immune system/viral protein Chain: K: PDB Molecule:envelope glycoprotein gp1; PDBTitle: crystal structure of the trimeric prefusion ebola virus glycoprotein2 in complex with a neutralizing antibody from a human survivor 31 d2aw0a_ not modelled 6.8 18 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 32 c1y3kA_ not modelled 6.3 9 PDB header:hydrolase Chain: A: PDB Molecule:copper-transporting atpase 1; PDBTitle: solution structure of the apo form of the fifth domain of2 menkes protein 33 d2ggpb1 not modelled 6.2 17 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 34 c3q94B_ not modelled 6.2 41 PDB header:lyase Chain: B: PDB Molecule:fructose-bisphosphate aldolase, class ii; PDBTitle: the crystal structure of fructose 1,6-bisphosphate aldolase from2 bacillus anthracis str. 'ames ancestor' 35 c3a58A_ not modelled 6.0 16 PDB header:protein transport/exocytosis Chain: A: PDB Molecule:exocyst complex component sec3; PDBTitle: crystal structure of sec3p - rho1p complex from2 saccharomyces cerevisiae 36 c2r39A_ not modelled 5.9 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:fixg-related protein; PDBTitle: crystal structure of fixg-related protein from vibrio parahaemolyticus 37 c2i7dB_ not modelled 5.7 56 PDB header:hydrolase Chain: B: PDB Molecule:5'(3')-deoxyribonucleotidase, cytosolic type; PDBTitle: structure of human cytosolic deoxyribonucleotidase in2 complex with deoxyuridine, alf4 and mg2+ 38 d1p6ta1 not modelled 5.6 17 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 39 c2kt2A_ not modelled 5.3 24 PDB header:oxidoreductase Chain: A: PDB Molecule:mercuric reductase; PDBTitle: structure of nmera, the n-terminal hma domain of tn501 mercuric2 reductase 40 c3n1hA_ not modelled 5.3 20 PDB header:dna binding protein Chain: A: PDB Molecule:stwhy2; PDBTitle: crystal structure of stwhy2 41 c3cqrB_ not modelled 5.3 24 PDB header:oxidoreductase Chain: B: PDB Molecule:violaxanthin de-epoxidase, chloroplast; PDBTitle: crystal structure of the lipocalin domain of violaxanthin2 de-epoxidase (vde) at ph5 42 c3fwaA_ not modelled 5.1 15 PDB header:flavoprotein Chain: A: PDB Molecule:reticuline oxidase; PDBTitle: structure of berberine bridge enzyme, c166a variant in complex with2 (s)-reticuline

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