Secondary structure and disorder prediction

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Sequence		M	P	V	I	K	V	R	E	N	E	P	F	D	V	A	L	R	R	F	K	R	S	C	E	K	A	G	V	L	A	E	V	R	R	R	E	F	Y	E	K	P	T	T	E	R	K	R	A	K	A	S	A	V	K	R	H	A	K	K	L
Secondary structure
SS confidence
Disorder		?	?	?			?	?																														?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.
Sequence		A	R	E	N	A	R	R	T	R	L	Y
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 2z4m chain U Region: 4 - 54 Aligned: 51 Modelled: 51 Confidence: 99.8% Identity: 100% PDB header:ribosome Chain: U: PDB Molecule:30s ribosomal protein s21; PDBTitle: crystal structure of the bacterial ribosome from escherichia2 coli in complex with paromomycin and ribosome recycling3 factor (rrf). this file contains the 30s subunit of the4 second 70s ribosome, with paromomycin bound. the entire5 crystal structure contains two 70s ribosomes and is6 described in remark 400. Phyre2 PDB 3bbn chain U Region: 2 - 54 Aligned: 53 Modelled: 53 Confidence: 99.8% Identity: 40% PDB header:ribosome Chain: U: PDB Molecule:ribosomal protein s21; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 3fih chain U Region: 4 - 54 Aligned: 51 Modelled: 51 Confidence: 99.8% Identity: 100% PDB header:ribosome Chain: U: PDB Molecule:30s ribosomal protein s21; PDBTitle: ternary complex-bound e.coli 70s ribosome. this entry2 consists of the 30s subunit, trnas and the ternary complex. Phyre2 PDB 1edz chain A domain 2 Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 39.7% Identity: 7% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Tetrahydrofolate dehydrogenase/cyclohydrolase Phyre2 PDB 1a4i chain A domain 2 Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 33.8% Identity: 11% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Tetrahydrofolate dehydrogenase/cyclohydrolase Phyre2 PDB 1b0a chain A domain 2 Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 28.5% Identity: 21% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Tetrahydrofolate dehydrogenase/cyclohydrolase Phyre2 PDB 1bvu chain A domain 2 Region: 9 - 28 Aligned: 20 Modelled: 20 Confidence: 24.0% Identity: 20% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Aminoacid dehydrogenases Phyre2 PDB 2eia chain A domain 1 Region: 4 - 34 Aligned: 31 Modelled: 31 Confidence: 23.1% Identity: 19% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 1eoq chain A Region: 4 - 33 Aligned: 30 Modelled: 30 Confidence: 22.2% Identity: 20% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 1qrj chain B domain 1 Region: 4 - 25 Aligned: 22 Modelled: 22 Confidence: 18.0% Identity: 18% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 3ngl chain A Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 15.6% Identity: 25% PDB header:oxidoreductase, hydrolase Chain: A: PDB Molecule:bifunctional protein fold; PDBTitle: crystal structure of bifunctional 5,10-methylenetetrahydrofolate2 dehydrogenase / cyclohydrolase from thermoplasma acidophilum Phyre2 PDB 1edz chain A Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 15.2% Identity: 7% PDB header:oxidoreductase Chain: A: PDB Molecule:5,10-methylenetetrahydrofolate dehydrogenase; PDBTitle: structure of the nad-dependent 5,10-2 methylenetetrahydrofolate dehydrogenase from saccharomyces3 cerevisiae Phyre2 PDB 1b0a chain A Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 14.8% Identity: 21% PDB header:oxidoreductase,hydrolase Chain: A: PDB Molecule:protein (fold bifunctional protein); PDBTitle: 5,10, methylene-tetrahydropholate2 dehydrogenase/cyclohydrolase from e coli. Phyre2 PDB 1q9u chain A Region: 1 - 27 Aligned: 27 Modelled: 27 Confidence: 13.9% Identity: 19% Fold: TBP-like Superfamily: TT1751-like Family: TT1751-like Phyre2 PDB 1a4i chain B Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 13.8% Identity: 11% PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase / PDBTitle: human tetrahydrofolate dehydrogenase / cyclohydrolase Phyre2 PDB 2c2x chain B Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 13.5% Identity: 21% PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase- PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis Phyre2 PDB 3aog chain A Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 13.4% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:glutamate dehydrogenase; PDBTitle: crystal structure of glutamate dehydrogenase (gdhb) from thermus2 thermophilus (glu bound form) Phyre2 PDB 3fiq chain A Region: 1 - 31 Aligned: 31 Modelled: 31 Confidence: 13.1% Identity: 6% PDB header:transport protein Chain: A: PDB Molecule:odorant-binding protein 1f; PDBTitle: odorant binding protein obp1 Phyre2 PDB 1d1d chain A domain 1 Region: 2 - 26 Aligned: 25 Modelled: 25 Confidence: 13.1% Identity: 20% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 2k1c chain A Region: 4 - 33 Aligned: 30 Modelled: 30 Confidence: 13.1% Identity: 27% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:capsid protein p24; PDBTitle: nmr structure of the c-terminal domain of hiv-1 capsid in complex with2 peptide inhibitor Phyre2 1 c2z4mU_ 2 c3bbnU_ 3 c3fihU_ 4 d1edza2 5 d1a4ia2 6 d1b0aa2 7 d1bvua2 8 d2eiaa1 9 d1eoqa_ 10 d1qrjb1 11 c3nglA_ 12 c1edzA_ 13 c1b0aA_ 14 d1q9ua_ 15 c1a4iB_ 16 c2c2xB_ 17 c3aogA_ 18 c3fiqA_ 19 d1d1da1 20 c2k1cA_ 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

Detailed template information

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

1 c2z4mU_ 99.8 100 PDB header:ribosome Chain: U: PDB Molecule:30s ribosomal protein s21; PDBTitle: crystal structure of the bacterial ribosome from escherichia2 coli in complex with paromomycin and ribosome recycling3 factor (rrf). this file contains the 30s subunit of the4 second 70s ribosome, with paromomycin bound. the entire5 crystal structure contains two 70s ribosomes and is6 described in remark 400. 2 c3bbnU_ 99.8 40 PDB header:ribosome Chain: U: PDB Molecule:ribosomal protein s21; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 3 c3fihU_ 99.8 100 PDB header:ribosome Chain: U: PDB Molecule:30s ribosomal protein s21; PDBTitle: ternary complex-bound e.coli 70s ribosome. this entry2 consists of the 30s subunit, trnas and the ternary complex. 4 d1edza2 39.7 7 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Tetrahydrofolate dehydrogenase/cyclohydrolase 5 d1a4ia2 33.8 11 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Tetrahydrofolate dehydrogenase/cyclohydrolase 6 d1b0aa2 28.5 21 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Tetrahydrofolate dehydrogenase/cyclohydrolase 7 d1bvua2 24.0 20 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 8 d2eiaa1 23.1 19 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 9 d1eoqa_ 22.2 20 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 10 d1qrjb1 18.0 18 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 11 c3nglA_ 15.6 25 PDB header:oxidoreductase, hydrolase Chain: A: PDB Molecule:bifunctional protein fold; PDBTitle: crystal structure of bifunctional 5,10-methylenetetrahydrofolate2 dehydrogenase / cyclohydrolase from thermoplasma acidophilum 12 c1edzA_ 15.2 7 PDB header:oxidoreductase Chain: A: PDB Molecule:5,10-methylenetetrahydrofolate dehydrogenase; PDBTitle: structure of the nad-dependent 5,10-2 methylenetetrahydrofolate dehydrogenase from saccharomyces3 cerevisiae 13 c1b0aA_ 14.8 21 PDB header:oxidoreductase,hydrolase Chain: A: PDB Molecule:protein (fold bifunctional protein); PDBTitle: 5,10, methylene-tetrahydropholate2 dehydrogenase/cyclohydrolase from e coli. 14 d1q9ua_ 13.9 19 Fold:TBP-like Superfamily:TT1751-like Family:TT1751-like 15 c1a4iB_ 13.8 11 PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase / PDBTitle: human tetrahydrofolate dehydrogenase / cyclohydrolase 16 c2c2xB_ 13.5 21 PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase- PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis 17 c3aogA_ 13.4 14 PDB header:oxidoreductase Chain: A: PDB Molecule:glutamate dehydrogenase; PDBTitle: crystal structure of glutamate dehydrogenase (gdhb) from thermus2 thermophilus (glu bound form) 18 c3fiqA_ 13.1 6 PDB header:transport protein Chain: A: PDB Molecule:odorant-binding protein 1f; PDBTitle: odorant binding protein obp1 19 d1d1da1 13.1 20 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 20 c2k1cA_ 13.1 27 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:capsid protein p24; PDBTitle: nmr structure of the c-terminal domain of hiv-1 capsid in complex with2 peptide inhibitor 21 c1bajA_ not modelled 12.7 27 PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: hiv-1 capsid protein c-terminal fragment plus gag p2 domain 22 c4a5oB_ not modelled 12.2 25 PDB header:oxidoreductase Chain: B: PDB Molecule:bifunctional protein fold; PDBTitle: crystal structure of pseudomonas aeruginosa n5, n10-2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase (fold) 23 d1e5pa_ not modelled 11.9 10 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 24 c3p2oA_ not modelled 11.4 25 PDB header:oxidoreductase, hydrolase Chain: A: PDB Molecule:bifunctional protein fold; PDBTitle: crystal structure of fold bifunctional protein from campylobacter2 jejuni 25 d1p94a_ not modelled 10.8 33 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 26 c3couA_ not modelled 10.5 24 PDB header:hydrolase Chain: A: PDB Molecule:nucleoside diphosphate-linked moiety x motif 16; PDBTitle: crystal structure of human nudix motif 16 (nudt16) 27 d1gtma2 not modelled 10.4 12 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 28 c3kvhA_ not modelled 10.3 24 PDB header:rna binding protein Chain: A: PDB Molecule:protein syndesmos; PDBTitle: crystal structure of human protein syndesmos (nudt16-like protein) 29 c3p2oB_ not modelled 9.7 25 PDB header:oxidoreductase, hydrolase Chain: B: PDB Molecule:bifunctional protein fold; PDBTitle: crystal structure of fold bifunctional protein from campylobacter2 jejuni 30 c3l07B_ not modelled 9.6 14 PDB header:oxidoreductase,hydrolase Chain: B: PDB Molecule:bifunctional protein fold; PDBTitle: methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate2 cyclohydrolase, putative bifunctional protein fold from francisella3 tularensis. 31 c2k87A_ not modelled 9.6 14 PDB header:viral protein, rna binding protein Chain: A: PDB Molecule:non-structural protein 3 of replicase polyprotein 1a; PDBTitle: nmr structure of a putative rna binding protein (sars1) from sars2 coronavirus 32 c3gwyA_ not modelled 9.4 44 PDB header:hydrolase Chain: A: PDB Molecule:putative ctp pyrophosphohydrolase; PDBTitle: crystal structure of putative ctp pyrophosphohydrolase from2 bacteroides fragilis 33 c2jobA_ not modelled 9.2 14 PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site 34 c4a26B_ not modelled 8.7 11 PDB header:oxidoreductase Chain: B: PDB Molecule:putative c-1-tetrahydrofolate synthase, cytoplasmic; PDBTitle: the crystal structure of leishmania major n5,n10-2 methylenetetrahydrofolate dehydrogenase/cyclohydrolase 35 d1a8oa_ not modelled 8.5 27 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 36 d1dzka_ not modelled 8.3 21 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 37 c2x8qA_ not modelled 8.1 20 PDB header:virus Chain: A: PDB Molecule:capsid protein p27; PDBTitle: cryo-em 3d model of the icosahedral particle2 composed of rous sarcoma virus capsid protein pentamers 38 d1euza2 not modelled 7.7 20 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 39 d1bj7a_ not modelled 7.3 16 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 40 c1qrjB_ not modelled 7.1 16 PDB header:viral protein Chain: B: PDB Molecule:htlv-i capsid protein; PDBTitle: solution structure of htlv-i capsid protein 41 c2yfqA_ not modelled 7.1 27 PDB header:oxidoreductase Chain: A: PDB Molecule:nad-specific glutamate dehydrogenase; PDBTitle: crystal structure of glutamate dehydrogenase from2 peptoniphilus asaccharolyticus 42 c3kwlA_ not modelled 6.5 24 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a hypothetical protein from helicobacter pylori 43 c2r73C_ not modelled 6.1 16 PDB header:transport protein Chain: C: PDB Molecule:trichosurin; PDBTitle: crystal structure of the possum milk whey lipocalin2 trichosurin at ph 8.2 44 c1d1dA_ not modelled 5.9 23 PDB header:viral protein Chain: A: PDB Molecule:protein (capsid protein); PDBTitle: nmr solution structure of the capsid protein from rous2 sarcoma virus 45 d1igna2 not modelled 5.9 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:DNA-binding domain of rap1 46 c2fb1A_ not modelled 5.9 28 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of protein bt0354 from bacteroides thetaiotaomicron 47 c3stgA_ not modelled 5.2 23 PDB header:transferase Chain: A: PDB Molecule:2-dehydro-3-deoxyphosphooctonate aldolase; PDBTitle: crystal structure of a58p, del(n59), and loop 7 truncated mutant of 3-2 deoxy-d-manno-octulosonate 8-phosphate synthase (kdo8ps) from3 neisseria meningitidis 48 c1bvuF_ not modelled 5.2 19 PDB header:oxidoreductase Chain: F: PDB Molecule:protein (glutamate dehydrogenase); PDBTitle: glutamate dehydrogenase from thermococcus litoralis

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