Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	I	Q	C	K	R	V	Y	D	P	A	E	Q	S	D	G	Y	R	I	L	V	D	R	L	W	P	R	G	I	K	K	T	D	L	A	L	D	E	W	D	K	E	I	T	P	S	T	E	L	R	K	A	F	H	G	E	V	V	D
Secondary structure
SS confidence
Disorder		?	?	?																																																				?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.
Sequence		Y	A	T	F	R	E	Q	Y	L	A	E	L	A	Q	H	E	Q	E	G	K	R	L	A	D	I	A	K	K	Q	P	L	T	L	L	Y	S	A	K	N	T	T	Q	N	H	A	L	V	L	A	D	W	L	R	S	L
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 1e8c chain A domain 2 Region: 76 - 115 Aligned: 40 Modelled: 40 Confidence: 29.2% Identity: 13% Fold: MurD-like peptide ligases, peptide-binding domain Superfamily: MurD-like peptide ligases, peptide-binding domain Family: MurCDEF C-terminal domain Phyre2 PDB 1bsm chain A domain 2 Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 22.0% Identity: 23% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2gyk chain B domain 1 Region: 60 - 82 Aligned: 23 Modelled: 23 Confidence: 17.9% Identity: 22% Fold: His-Me finger endonucleases Superfamily: His-Me finger endonucleases Family: HNH-motif Phyre2 PDB 1sh0 chain A Region: 48 - 76 Aligned: 29 Modelled: 29 Confidence: 16.1% Identity: 21% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2b43 chain D Region: 48 - 75 Aligned: 28 Modelled: 28 Confidence: 15.8% Identity: 21% PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge Phyre2 PDB 2nyb chain A domain 2 Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 15.3% Identity: 19% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1y67 chain A domain 2 Region: 46 - 70 Aligned: 25 Modelled: 25 Confidence: 15.3% Identity: 24% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1ids chain A domain 2 Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 15.1% Identity: 31% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2c55 chain A Region: 42 - 60 Aligned: 19 Modelled: 19 Confidence: 15.0% Identity: 32% PDB header:viral protein Chain: A: PDB Molecule:protein p6; PDBTitle: solution structure of the human immunodeficiency virus type2 1 p6 protein Phyre2 PDB 3nah chain C Region: 48 - 75 Aligned: 28 Modelled: 28 Confidence: 14.7% Identity: 25% PDB header:transferase Chain: C: PDB Molecule:rna dependent rna polymerase; PDBTitle: crystal structures and functional analysis of murine norovirus rna-2 dependent rna polymerase Phyre2 PDB 1jr9 chain A domain 2 Region: 45 - 74 Aligned: 30 Modelled: 30 Confidence: 12.8% Identity: 20% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1gv3 chain A domain 2 Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 12.3% Identity: 12% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1ix9 chain A domain 2 Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 12.2% Identity: 15% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1wb8 chain A domain 2 Region: 46 - 74 Aligned: 29 Modelled: 29 Confidence: 12.1% Identity: 10% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2zfu chain A Region: 45 - 74 Aligned: 30 Modelled: 30 Confidence: 11.6% Identity: 10% PDB header:nuclear protein Chain: A: PDB Molecule:cerebral protein 1; PDBTitle: structure of the methyltransferase-like domain of nucleomethylin Phyre2 PDB 1p7g chain A domain 2 Region: 46 - 70 Aligned: 25 Modelled: 25 Confidence: 10.5% Identity: 12% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1uer chain A domain 2 Region: 42 - 70 Aligned: 29 Modelled: 29 Confidence: 10.1% Identity: 21% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1coj chain A domain 2 Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 9.7% Identity: 19% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1b06 chain A domain 2 Region: 46 - 74 Aligned: 29 Modelled: 29 Confidence: 9.7% Identity: 10% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2jng chain A domain 1 Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 9.5% Identity: 13% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: CPH domain Phyre2 1 d1e8ca2 2 d1bsma2 3 d2gykb1 4 d1sh0a_ 5 c2b43D_ 6 d2nyba2 7 d1y67a2 8 d1idsa2 9 c2c55A_ 10 c3nahC_ 11 d1jr9a2 12 d1gv3a2 13 d1ix9a2 14 d1wb8a2 15 c2zfuA_ 16 d1p7ga2 17 d1uera2 18 d1coja2 19 d1b06a2 20 d2jnga1 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

Detailed template information

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

1 d1e8ca2 29.2 13 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 2 d1bsma2 22.0 23 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 3 d2gykb1 17.9 22 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif 4 d1sh0a_ 16.1 21 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 5 c2b43D_ 15.8 21 PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge 6 d2nyba2 15.3 19 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 7 d1y67a2 15.3 24 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 8 d1idsa2 15.1 31 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 9 c2c55A_ 15.0 32 PDB header:viral protein Chain: A: PDB Molecule:protein p6; PDBTitle: solution structure of the human immunodeficiency virus type2 1 p6 protein 10 c3nahC_ 14.7 25 PDB header:transferase Chain: C: PDB Molecule:rna dependent rna polymerase; PDBTitle: crystal structures and functional analysis of murine norovirus rna-2 dependent rna polymerase 11 d1jr9a2 12.8 20 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 12 d1gv3a2 12.3 12 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 13 d1ix9a2 12.2 15 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 14 d1wb8a2 12.1 10 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 15 c2zfuA_ 11.6 10 PDB header:nuclear protein Chain: A: PDB Molecule:cerebral protein 1; PDBTitle: structure of the methyltransferase-like domain of nucleomethylin 16 d1p7ga2 10.5 12 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 17 d1uera2 10.1 21 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 18 d1coja2 9.7 19 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 19 d1b06a2 9.7 10 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 20 d2jnga1 9.5 13 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:CPH domain 21 c2xznT_ not modelled 9.5 19 PDB header:ribosome Chain: T: PDB Molecule:rps19e; 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 2 22 c2jufA_ not modelled 9.3 13 PDB header:gene regulation Chain: A: PDB Molecule:p53-associated parkin-like cytoplasmic protein; PDBTitle: nmr solution structure of parc cph domain. nesg target2 hr3443b/sgc-toronto 23 c2k4nA_ not modelled 9.2 35 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein pf0246; PDBTitle: nmr structure of protein pf0246 from pyrococcus furiosus:2 target pfr75 from the northeast structural genomics3 consortium 24 d1unfx2 not modelled 8.7 24 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 25 d2jb0b1 not modelled 8.5 19 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif 26 c7ceiB_ not modelled 8.5 19 PDB header:immune system Chain: B: PDB Molecule:protein (colicin e7 immunity protein); PDBTitle: the endonuclease domain of colicin e7 in complex with its inhibitor2 im7 protein 27 d2p4ka2 not modelled 8.4 23 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 28 d1my6a2 not modelled 8.1 16 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 29 c3h4rA_ not modelled 7.5 47 PDB header:hydrolase Chain: A: PDB Molecule:exodeoxyribonuclease 8; PDBTitle: crystal structure of e. coli rece exonuclease 30 d3sdpa2 not modelled 7.5 19 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 31 c3bl9B_ not modelled 7.4 31 PDB header:hydrolase Chain: B: PDB Molecule:scavenger mrna-decapping enzyme dcps; PDBTitle: synthetic gene encoded dcps bound to inhibitor dg157493 32 d1mnga2 not modelled 7.1 23 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 33 c3iz6S_ not modelled 7.1 26 PDB header:ribosome Chain: S: PDB Molecule:40s ribosomal protein s19 (s19e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 34 c3iz5N_ not modelled 7.1 43 PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein l14 (l14e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 35 c1xmlA_ not modelled 7.0 31 PDB header:chaperone Chain: A: PDB Molecule:heat shock-like protein 1; PDBTitle: structure of human dcps 36 d1ohua_ not modelled 6.9 9 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 37 c2jofA_ not modelled 6.4 38 PDB header:de novo protein Chain: A: PDB Molecule:trp-cage; PDBTitle: the trp-cage: optimizing the stability of a globular2 miniprotein 38 d1u09a_ not modelled 6.3 21 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 39 c2kzuA_ not modelled 6.2 22 PDB header:apoptosis Chain: A: PDB Molecule:death-associated protein 6; PDBTitle: daxx helical bundle (dhb) domain / rassf1c complex 40 c1b06A_ not modelled 6.1 12 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (superoxide dismutase); PDBTitle: superoxide dismutase from sulfolobus acidocaldarius 41 c1y6uA_ not modelled 5.8 33 PDB header:dna binding protein Chain: A: PDB Molecule:excisionase from transposon tn916; PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases 42 d1iufa1 not modelled 5.6 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 43 c2nybC_ not modelled 5.6 19 PDB header:oxidoreductase Chain: C: PDB Molecule:superoxide dismutase [fe]; PDBTitle: crystal structure of e.coli iron superoxide dismutase q69e2 at 1.1 angstrom resolution 44 d1dt0a2 not modelled 5.6 17 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 45 c1avmA_ not modelled 5.5 23 PDB header:oxidoreductase Chain: A: PDB Molecule:superoxide dismutase; PDBTitle: the cambialistic superoxide dismutase (fe-sod) of p. shermanii2 coordinated by azide 46 c2cw2B_ not modelled 5.3 16 PDB header:oxidoreductase Chain: B: PDB Molecule:superoxide dismutase 1; PDBTitle: crystal structure of superoxide dismutase from p. marinus 47 c3tqjB_ not modelled 5.3 24 PDB header:oxidoreductase Chain: B: PDB Molecule:superoxide dismutase [fe]; PDBTitle: structure of the superoxide dismutase (fe) (sodb) from coxiella2 burnetii 48 d1vlra1 not modelled 5.2 31 Fold:HIT-like Superfamily:HIT-like Family:mRNA decapping enzyme DcpS C-terminal domain 49 c1my6A_ not modelled 5.2 15 PDB header:oxidoreductase Chain: A: PDB Molecule:iron (iii) superoxide dismutase; PDBTitle: the 1.6 a structure of fe-superoxide dismutase from the2 thermophilic cyanobacterium thermosynechococcus elongatus3 : correlation of epr and structural characteristics 50 c2gpcB_ not modelled 5.2 15 PDB header:oxidoreductase Chain: B: PDB Molecule:iron superoxide dismutase; PDBTitle: the crystal structure of the enzyme fe-superoxide dismutase2 from trypanosoma cruzi 51 c2a03A_ not modelled 5.2 16 PDB header:oxidoreductase Chain: A: PDB Molecule:fe-superoxide dismutase homolog; PDBTitle: superoxide dismutase protein from plasmodium berghei 52 c1ma1E_ not modelled 5.1 19 PDB header:oxidoreductase Chain: E: PDB Molecule:superoxide dismutase; PDBTitle: structure and properties of the atypical iron superoxide2 dismutase from methanobacterium thermoautotrophicum

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