Secondary structure and disorder prediction

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10

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20

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30

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40

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50

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60

Sequence

M

A

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V

N

Q

L

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R

K

P

R

A

R

K

V

A

K

S

N

V

P

A

L

E

A

C

P

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K

R

G

V

C

T

R

V

Y

T

T

T

P

K

K

P

N

S

A

L

R

K

V

C

R

V

R

L

T

N

G

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

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90

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100

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110

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120

Sequence

F

E

V

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S

Y

I

G

G

E

G

H

N

L

Q

E

H

S

V

I

L

I

R

G

G

R

V

K

D

L

P

G

V

R

Y

H

T

V

R

G

A

L

D

C

S

G

V

K

D

R

K

Q

A

R

S

K

Y

G

V

K

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

R

P

K

A

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 2qal chain L domain 1 Region: 2 - 124 Aligned: 123 Modelled: 123 Confidence: 100.0% Identity: 100% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1i94 chain L Region: 2 - 124 Aligned: 123 Modelled: 123 Confidence: 100.0% Identity: 72% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2uub chain L domain 1 Region: 2 - 119 Aligned: 118 Modelled: 118 Confidence: 100.0% Identity: 73% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1zn1 chain L Region: 28 - 124 Aligned: 97 Modelled: 97 Confidence: 100.0% Identity: 100% PDB header:biosynthetic/structural protein/rna Chain: L: PDB Molecule:30s ribosomal protein s12; PDBTitle: coordinates of rrf fitted into cryo-em map of the 70s post-2 termination complex Phyre2 PDB 2xzm chain L Region: 1 - 114 Aligned: 114 Modelled: 113 Confidence: 100.0% Identity: 28% PDB header:ribosome Chain: L: PDB Molecule:40s ribosomal protein s12; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 2zkq chain L Region: 11 - 113 Aligned: 103 Modelled: 103 Confidence: 100.0% Identity: 27% PDB header:ribosomal protein/rna Chain: L: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1s1h chain L Region: 11 - 113 Aligned: 103 Modelled: 103 Confidence: 100.0% Identity: 29% PDB header:ribosome Chain: L: PDB Molecule:40s ribosomal protein s23; 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. Phyre2 PDB 3i4o chain A Region: 54 - 83 Aligned: 30 Modelled: 30 Confidence: 85.1% Identity: 23% PDB header:translation Chain: A: PDB Molecule:translation initiation factor if-1; PDBTitle: crystal structure of translation initiation factor 1 from2 mycobacterium tuberculosis Phyre2 PDB 1ah9 chain A Region: 54 - 83 Aligned: 30 Modelled: 30 Confidence: 85.0% Identity: 30% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1hr0 chain W Region: 54 - 83 Aligned: 30 Modelled: 30 Confidence: 69.8% Identity: 27% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1jt8 chain A Region: 54 - 69 Aligned: 16 Modelled: 16 Confidence: 45.4% Identity: 38% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2oqk chain A Region: 54 - 69 Aligned: 16 Modelled: 16 Confidence: 37.8% Identity: 19% PDB header:translation Chain: A: PDB Molecule:putative translation initiation factor eif-1a; PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a Phyre2 PDB 2ix0 chain A domain 3 Region: 54 - 99 Aligned: 44 Modelled: 46 Confidence: 29.8% Identity: 41% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2d1c chain B Region: 57 - 71 Aligned: 15 Modelled: 15 Confidence: 27.8% Identity: 33% PDB header:oxidoreductase Chain: B: PDB Molecule:isocitrate dehydrogenase; PDBTitle: crystal structure of tt0538 protein from thermus thermophilus hb8 Phyre2 PDB 1d7q chain A Region: 53 - 83 Aligned: 31 Modelled: 31 Confidence: 26.9% Identity: 16% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1v7w chain A domain 1 Region: 36 - 84 Aligned: 47 Modelled: 49 Confidence: 24.0% Identity: 19% Fold: alpha/alpha toroid Superfamily: Six-hairpin glycosidases Family: Glycosyltransferase family 36 C-terminal domain Phyre2 PDB 1y80 chain A Region: 58 - 74 Aligned: 17 Modelled: 17 Confidence: 22.9% Identity: 24% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted cobalamin binding protein; PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica Phyre2 PDB 1ju2 chain A domain 1 Region: 58 - 77 Aligned: 20 Modelled: 20 Confidence: 19.0% Identity: 15% Fold: FAD/NAD(P)-binding domain Superfamily: FAD/NAD(P)-binding domain Family: FAD-linked reductases, N-terminal domain Phyre2 PDB 1ear chain A domain 1 Region: 48 - 87 Aligned: 39 Modelled: 40 Confidence: 15.9% Identity: 13% Fold: Urease metallochaperone UreE, N-terminal domain Superfamily: Urease metallochaperone UreE, N-terminal domain Family: Urease metallochaperone UreE, N-terminal domain Phyre2 PDB 1pb1 chain A Region: 54 - 71 Aligned: 18 Modelled: 18 Confidence: 15.7% Identity: 44% Fold: Isocitrate/Isopropylmalate dehydrogenase-like Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like Family: Dimeric isocitrate & isopropylmalate dehydrogenases Phyre2 1 d2qall1 2 d1i94l_ 3 d2uubl1 4 c1zn1L_ 5 c2xzmL_ 6 c2zkql_ 7 c1s1hL_ 8 c3i4oA_ 9 d1ah9a_ 10 d1hr0w_ 11 d1jt8a_ 12 c2oqkA_ 13 d2ix0a3 14 c2d1cB_ 15 d1d7qa_ 16 d1v7wa1 17 c1y80A_ 18 d1ju2a1 19 d1eara1 20 d1pb1a_ 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

Detailed template information

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

1 d2qall1 100.0 100 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 2 d1i94l_ 100.0 72 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 3 d2uubl1 100.0 73 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 4 c1zn1L_ 100.0 100 PDB header:biosynthetic/structural protein/rna Chain: L: PDB Molecule:30s ribosomal protein s12; PDBTitle: coordinates of rrf fitted into cryo-em map of the 70s post-2 termination complex 5 c2xzmL_ 100.0 28 PDB header:ribosome Chain: L: PDB Molecule:40s ribosomal protein s12; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 6 c2zkql_ 100.0 27 PDB header:ribosomal protein/rna Chain: L: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 7 c1s1hL_ 100.0 29 PDB header:ribosome Chain: L: PDB Molecule:40s ribosomal protein s23; 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. 8 c3i4oA_ 85.1 23 PDB header:translation Chain: A: PDB Molecule:translation initiation factor if-1; PDBTitle: crystal structure of translation initiation factor 1 from2 mycobacterium tuberculosis 9 d1ah9a_ 85.0 30 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 10 d1hr0w_ 69.8 27 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 11 d1jt8a_ 45.4 38 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 12 c2oqkA_ 37.8 19 PDB header:translation Chain: A: PDB Molecule:putative translation initiation factor eif-1a; PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a 13 d2ix0a3 29.8 41 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 14 c2d1cB_ 27.8 33 PDB header:oxidoreductase Chain: B: PDB Molecule:isocitrate dehydrogenase; PDBTitle: crystal structure of tt0538 protein from thermus thermophilus hb8 15 d1d7qa_ 26.9 16 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 16 d1v7wa1 24.0 19 Fold:alpha/alpha toroid Superfamily:Six-hairpin glycosidases Family:Glycosyltransferase family 36 C-terminal domain 17 c1y80A_ 22.9 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted cobalamin binding protein; PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica 18 d1ju2a1 19.0 15 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD-linked reductases, N-terminal domain 19 d1eara1 15.9 13 Fold:Urease metallochaperone UreE, N-terminal domain Superfamily:Urease metallochaperone UreE, N-terminal domain Family:Urease metallochaperone UreE, N-terminal domain 20 d1pb1a_ 15.7 44 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases 21 d3bula2 not modelled 13.6 35 Fold:Flavodoxin-like Superfamily:Cobalamin (vitamin B12)-binding domain Family:Cobalamin (vitamin B12)-binding domain 22 d1o7ia_ not modelled 12.6 10 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 23 d1e32a1 not modelled 12.0 18 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Cdc48 N-terminal domain-like 24 d1yrra1 not modelled 12.0 29 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:N-acetylglucosamine-6-phosphate deacetylase, NagA 25 d1dwna_ not modelled 11.9 32 Fold:RNA bacteriophage capsid protein Superfamily:RNA bacteriophage capsid protein Family:RNA bacteriophage capsid protein 26 d1rutx4 not modelled 10.7 33 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 27 c2jx5A_ not modelled 10.0 16 PDB header:ribosomal protein Chain: A: PDB Molecule:glub(s27a); PDBTitle: solution structure of the ubiquitin domain n-terminal to2 the s27a ribosomal subunit of giardia lamblia 28 c3swnA_ not modelled 9.7 9 PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 29 d1hqsa_ not modelled 8.9 33 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases 30 d1rxta1 not modelled 8.2 18 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-myristoyl transferase, NMT 31 d2dipa1 not modelled 8.2 17 Fold:RING/U-box Superfamily:RING/U-box Family:ZZ domain 32 d2vo1a1 not modelled 8.0 32 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 33 c3n0vD_ not modelled 7.5 15 PDB header:hydrolase Chain: D: PDB Molecule:formyltetrahydrofolate deformylase; PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pp_0327)2 from pseudomonas putida kt2440 at 2.25 a resolution 34 d1x7fa2 not modelled 7.1 17 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Outer surface protein, N-terminal domain 35 d1ccwa_ not modelled 6.8 22 Fold:Flavodoxin-like Superfamily:Cobalamin (vitamin B12)-binding domain Family:Cobalamin (vitamin B12)-binding domain 36 d1w98b1 not modelled 6.6 38 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 37 d2fcta1 not modelled 6.5 24 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:PhyH-like 38 c2r8cB_ not modelled 6.4 23 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative amidohydrolase; PDBTitle: crystal structure of uncharacterized protein eaj56179 39 c3bw1A_ not modelled 6.3 9 PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm3; PDBTitle: crystal structure of homomeric yeast lsm3 exhibiting novel octameric2 ring organisation 40 c2e0cA_ not modelled 6.2 33 PDB header:oxidoreductase Chain: A: PDB Molecule:409aa long hypothetical nadp-dependent isocitrate PDBTitle: crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii2 strain7 at 2.0 a resolution 41 c3louB_ not modelled 6.1 16 PDB header:hydrolase Chain: B: PDB Molecule:formyltetrahydrofolate deformylase; PDBTitle: crystal structure of formyltetrahydrofolate deformylase (yp_105254.1)2 from burkholderia mallei atcc 23344 at 1.90 a resolution 42 c3cw1D_ not modelled 6.1 9 PDB header:splicing Chain: D: PDB Molecule:small nuclear ribonucleoprotein sm d3; PDBTitle: crystal structure of human spliceosomal u1 snrnp 43 c1xyr6_ not modelled 6.0 45 PDB header:virus Chain: 6: PDB Molecule:genome polyprotein, coat protein vp3; PDB Fragment:residues 620-630 PDBTitle: poliovirus 135s cell entry intermediate 44 d1d3ba_ not modelled 5.9 10 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 45 c3hx6A_ not modelled 5.6 25 PDB header:cell adhesion Chain: A: PDB Molecule:type 4 fimbrial biogenesis protein pily1; PDBTitle: crystal structure of pseudomonas aeruginosa pily1 c-terminal2 domain 46 c1x7fA_ not modelled 5.6 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:outer surface protein; PDBTitle: crystal structure of an uncharacterized b. cereus protein

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