Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	I	I	S	K	R	R	A	M	T	I	Y	R	Q	H	P	E	S	R	I	F	R	Y	C	T	G	K	Y	Q	W	H	G	S	V	C	H	Y	T	G	R	D	V	P	D	I	A	G	V	L	A	V	Y	A	E	R	R	Q	D	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?						?																																												?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.
Sequence		N	G	P	Y	T	C	L	M	S	I	T	L	N
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 2cqm chain A domain 1 Region: 41 - 70 Aligned: 30 Modelled: 30 Confidence: 58.6% Identity: 30% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 1gd8 chain A Region: 41 - 70 Aligned: 30 Modelled: 30 Confidence: 53.1% Identity: 30% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 2zjr chain K domain 1 Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 53.1% Identity: 25% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 3bbo chain P Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 34.8% Identity: 25% PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2qam chain N domain 1 Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 30.5% Identity: 29% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 1bnl chain A Region: 6 - 39 Aligned: 34 Modelled: 34 Confidence: 15.5% Identity: 18% Fold: C-type lectin-like Superfamily: C-type lectin-like Family: Endostatin Phyre2 PDB 2qh7 chain A Region: 18 - 27 Aligned: 10 Modelled: 10 Confidence: 12.3% Identity: 40% PDB header:metal binding protein Chain: A: PDB Molecule:zinc finger cdgsh-type domain 1; PDBTitle: mitoneet is a uniquely folded 2fe-2s outer mitochondrial membrane2 protein stabilized by pioglitazone Phyre2 PDB 3fnv chain B Region: 18 - 27 Aligned: 10 Modelled: 10 Confidence: 12.3% Identity: 40% PDB header:metal binding protein Chain: B: PDB Molecule:cdgsh iron sulfur domain-containing protein 2; PDBTitle: crystal structure of miner1: the redox-active 2fe-2s protein causative2 in wolfram syndrome 2 Phyre2 PDB 2gyr chain B Region: 16 - 28 Aligned: 13 Modelled: 13 Confidence: 11.2% Identity: 38% PDB header:hormone/growth factor Chain: B: PDB Molecule:neurotrophic factor artemin, isoform 3; PDBTitle: crystal structure of human artemin Phyre2 PDB 1ir1 chain S Region: 31 - 70 Aligned: 40 Modelled: 40 Confidence: 11.1% Identity: 25% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 2j7q chain A domain 1 Region: 1 - 59 Aligned: 48 Modelled: 59 Confidence: 8.7% Identity: 19% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: M48USP-like Phyre2 PDB 3fka chain D Region: 16 - 72 Aligned: 45 Modelled: 57 Confidence: 8.5% Identity: 13% PDB header:unknown function Chain: D: PDB Molecule:uncharacterized ntf-2 like protein; PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution Phyre2 PDB 1koe chain A Region: 8 - 39 Aligned: 32 Modelled: 32 Confidence: 8.4% Identity: 19% Fold: C-type lectin-like Superfamily: C-type lectin-like Family: Endostatin Phyre2 PDB 1ztx chain E domain 1 Region: 21 - 37 Aligned: 17 Modelled: 17 Confidence: 8.2% Identity: 12% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Class II viral fusion proteins C-terminal domain Phyre2 PDB 2wsf chain N Region: 6 - 61 Aligned: 55 Modelled: 56 Confidence: 7.3% Identity: 20% PDB header:photosynthesis Chain: N: PDB Molecule:photosystem i-n subunit; PDBTitle: improved model of plant photosystem i Phyre2 PDB 3egp chain A Region: 21 - 32 Aligned: 12 Modelled: 12 Confidence: 7.3% Identity: 25% PDB header:viral protein Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure analysis of dengue-1 envelope protein2 domain iii Phyre2 PDB 1ok8 chain A domain 1 Region: 21 - 37 Aligned: 17 Modelled: 17 Confidence: 6.8% Identity: 24% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Class II viral fusion proteins C-terminal domain Phyre2 PDB 2kzt chain A Region: 42 - 56 Aligned: 15 Modelled: 15 Confidence: 6.7% Identity: 20% PDB header:apoptosis Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: structure of the tandem ma-3 region of pdcd4 Phyre2 PDB 1hd2 chain A Region: 27 - 51 Aligned: 25 Modelled: 25 Confidence: 6.6% Identity: 12% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione peroxidase-like Phyre2 PDB 2o01 chain N Region: 6 - 61 Aligned: 55 Modelled: 56 Confidence: 5.9% Identity: 20% PDB header:photosynthesis Chain: N: PDB Molecule:photosystem i-n subunit; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 1 d2cqma1 2 d1gd8a_ 3 d2zjrk1 4 c3bboP_ 5 d2qamn1 6 d1bnla_ 7 c2qh7A_ 8 c3fnvB_ 9 c2gyrB_ 10 d1ir1s_ 11 d2j7qa1 12 c3fkaD_ 13 d1koea_ 14 d1ztxe1 15 c2wsfN_ 16 c3egpA_ 17 d1ok8a1 18 c2kztA_ 19 d1hd2a_ 20 c2o01N_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 d2cqma1 58.6 30 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 2 d1gd8a_ 53.1 30 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 3 d2zjrk1 53.1 25 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 4 c3bboP_ 34.8 25 PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 5 d2qamn1 30.5 29 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 6 d1bnla_ 15.5 18 Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Endostatin 7 c2qh7A_ 12.3 40 PDB header:metal binding protein Chain: A: PDB Molecule:zinc finger cdgsh-type domain 1; PDBTitle: mitoneet is a uniquely folded 2fe-2s outer mitochondrial membrane2 protein stabilized by pioglitazone 8 c3fnvB_ 12.3 40 PDB header:metal binding protein Chain: B: PDB Molecule:cdgsh iron sulfur domain-containing protein 2; PDBTitle: crystal structure of miner1: the redox-active 2fe-2s protein causative2 in wolfram syndrome 2 9 c2gyrB_ 11.2 38 PDB header:hormone/growth factor Chain: B: PDB Molecule:neurotrophic factor artemin, isoform 3; PDBTitle: crystal structure of human artemin 10 d1ir1s_ 11.1 25 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 11 d2j7qa1 8.7 19 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:M48USP-like 12 c3fkaD_ 8.5 13 PDB header:unknown function Chain: D: PDB Molecule:uncharacterized ntf-2 like protein; PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution 13 d1koea_ 8.4 19 Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Endostatin 14 d1ztxe1 8.2 12 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 15 c2wsfN_ 7.3 20 PDB header:photosynthesis Chain: N: PDB Molecule:photosystem i-n subunit; PDBTitle: improved model of plant photosystem i 16 c3egpA_ 7.3 25 PDB header:viral protein Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure analysis of dengue-1 envelope protein2 domain iii 17 d1ok8a1 6.8 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 18 c2kztA_ 6.7 20 PDB header:apoptosis Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: structure of the tandem ma-3 region of pdcd4 19 d1hd2a_ 6.6 12 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 20 c2o01N_ 5.9 20 PDB header:photosynthesis Chain: N: PDB Molecule:photosystem i-n subunit; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 21 c2riqA_ not modelled 5.9 15 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: crystal structure of the third zinc-binding domain of human parp-1 22 d2j01s1 not modelled 5.7 33 Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:Ribosomal protein L18 and S11 23 c3ccjU_ not modelled 5.7 23 PDB header:ribosome Chain: U: PDB Molecule:50s ribosomal protein l24e; PDBTitle: structure of anisomycin resistant 50s ribosomal subunit: 23s rrna2 mutation c2534u 24 d1vqou1 not modelled 5.6 23 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Ribosomal protein L24e 25 c2iosA_ not modelled 5.5 40 PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd42 (mouse); form 3 26 c2rg8A_ not modelled 5.5 20 PDB header:apoptosis, translation Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: crystal structure of programmed for cell death 4 middle ma32 domain 27 d1m9sa3 not modelled 5.4 18 Fold:SH3-like barrel Superfamily:Prokaryotic SH3-related domain Family:GW domain 28 c2h0pA_ not modelled 5.2 18 PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein; PDBTitle: nmr structure of the dengue-4 virus envelope protein domain2 iii 29 c3oe3B_ not modelled 5.1 16 PDB header:hydrolase inhibitor Chain: B: PDB Molecule:putative periplasmic protein; PDBTitle: crystal structure of plic-st, periplasmic lysozyme inhibitor of c-type2 lysozyme from salmonella typhimurium 30 d1pjwa_ not modelled 5.1 18 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 31 c2jqmA_ not modelled 5.1 18 PDB header:transferase Chain: A: PDB Molecule:envelope protein e; PDBTitle: yellow fever envelope protein domain iii nmr structure2 (s288-k398)

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