Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	N	Q	R	I	R	I	R	L	K	A	F	D	H	R	L	I	D	Q	A	T	A	E	I	V	E	T	A	K	R	T	G	A	Q	V	R	G	P	I	P	L	P	T	R	K	E	R	F	T	V	L	I	S	P	H	V	N	K	D
Secondary structure
SS confidence
Disorder		?	?	?																																			?																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.
Sequence		A	R	D	Q	Y	E	I	R	T	H	L	R	L	V	D	I	V	E	P	T	E	K	T	V	D	A	L	M	R	L	D	L	A	A	G	V	D	V	Q	I	S	L	G
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 2qal chain J domain 1 Region: 5 - 102 Aligned: 98 Modelled: 98 Confidence: 100.0% Identity: 100% Fold: Ferredoxin-like Superfamily: Ribosomal protein S10 Family: Ribosomal protein S10 Phyre2 PDB 3bbn chain J Region: 4 - 102 Aligned: 99 Modelled: 99 Confidence: 100.0% Identity: 54% PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 2uub chain J domain 1 Region: 5 - 101 Aligned: 97 Modelled: 97 Confidence: 100.0% Identity: 55% Fold: Ferredoxin-like Superfamily: Ribosomal protein S10 Family: Ribosomal protein S10 Phyre2 PDB 2xzn chain J Region: 1 - 103 Aligned: 102 Modelled: 103 Confidence: 100.0% Identity: 28% PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10 containing protein; 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 Phyre2 PDB 2zkq chain J Region: 5 - 101 Aligned: 96 Modelled: 97 Confidence: 100.0% Identity: 27% PDB header:ribosomal protein/rna Chain: J: 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 J Region: 5 - 100 Aligned: 95 Modelled: 96 Confidence: 100.0% Identity: 25% PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20; 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 3iz6 chain J Region: 2 - 102 Aligned: 100 Modelled: 100 Confidence: 100.0% Identity: 27% PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20 (s10p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 3r2c chain J Region: 4 - 102 Aligned: 78 Modelled: 78 Confidence: 99.9% Identity: 55% PDB header:transcription/rna Chain: J: PDB Molecule:30s ribosomal protein s10; PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna Phyre2 PDB 1xbp chain G domain 1 Region: 18 - 38 Aligned: 21 Modelled: 21 Confidence: 33.6% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 1fno chain A domain 3 Region: 2 - 33 Aligned: 32 Modelled: 32 Confidence: 19.9% Identity: 19% Fold: Ferredoxin-like Superfamily: Bacterial exopeptidase dimerisation domain Family: Bacterial exopeptidase dimerisation domain Phyre2 PDB 1hc8 chain A Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 15.5% Identity: 37% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 1mms chain A domain 1 Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 15.2% Identity: 37% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 1s1i chain K Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 12.6% Identity: 37% PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l12; 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, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. Phyre2 PDB 1vq8 chain I Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 11.4% Identity: 26% PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11p; PDBTitle: the structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound2 to the large ribosomal subunit of haloarcula marismortui Phyre2 PDB 1dbd chain A Region: 74 - 99 Aligned: 26 Modelled: 26 Confidence: 10.8% Identity: 12% Fold: Ferredoxin-like Superfamily: Viral DNA-binding domain Family: Viral DNA-binding domain Phyre2 PDB 2kl8 chain A Region: 6 - 42 Aligned: 37 Modelled: 37 Confidence: 10.3% Identity: 22% PDB header:de novo protein Chain: A: PDB Molecule:or15; PDBTitle: solution nmr structure of de novo designed ferredoxin-like2 fold protein, northeast structural genomics consortium3 target or15 Phyre2 PDB 2zkr chain I Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 9.8% Identity: 32% PDB header:ribosomal protein/rna Chain: I: PDB Molecule:rna expansion segment es15 part i; PDBTitle: structure of a mammalian ribosomal 60s 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 1s6x chain A Region: 46 - 56 Aligned: 11 Modelled: 11 Confidence: 9.4% Identity: 36% PDB header:toxin Chain: A: PDB Molecule:kvap channel; PDBTitle: solution structure of vstx Phyre2 PDB 2yqr chain A Region: 2 - 43 Aligned: 42 Modelled: 42 Confidence: 8.5% Identity: 17% PDB header:rna binding protein Chain: A: PDB Molecule:kiaa0907 protein; PDBTitle: solution structure of the kh domain in kiaa0907 protein Phyre2 PDB 1jqm chain A Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 8.2% Identity: 37% PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l11; PDBTitle: fitting of l11 protein and elongation factor g (ef-g) in2 the cryo-em map of e. coli 70s ribosome bound with ef-g,3 gdp and fusidic acid Phyre2 1 d2qalj1 2 c3bbnJ_ 3 d2uubj1 4 c2xznJ_ 5 c2zkqj_ 6 c1s1hJ_ 7 c3iz6J_ 8 c3r2cJ_ 9 d1xbpg1 10 d1fnoa3 11 d1hc8a_ 12 d1mmsa1 13 c1s1iK_ 14 c1vq8I_ 15 d1dbda_ 16 c2kl8A_ 17 c2zkri_ 18 c1s6xA_ 19 c2yqrA_ 20 c1jqmA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d2qalj1 100.0 100 Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10 2 c3bbnJ_ 100.0 54 PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 3 d2uubj1 100.0 55 Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10 4 c2xznJ_ 100.0 28 PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10 containing protein; 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 5 c2zkqj_ 100.0 27 PDB header:ribosomal protein/rna Chain: J: 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 6 c1s1hJ_ 100.0 25 PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20; 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. 7 c3iz6J_ 100.0 27 PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20 (s10p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 8 c3r2cJ_ 99.9 55 PDB header:transcription/rna Chain: J: PDB Molecule:30s ribosomal protein s10; PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna 9 d1xbpg1 33.6 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 10 d1fnoa3 19.9 19 Fold:Ferredoxin-like Superfamily:Bacterial exopeptidase dimerisation domain Family:Bacterial exopeptidase dimerisation domain 11 d1hc8a_ 15.5 37 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 12 d1mmsa1 15.2 37 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 13 c1s1iK_ 12.6 37 PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l12; 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, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 14 c1vq8I_ 11.4 26 PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11p; PDBTitle: the structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound2 to the large ribosomal subunit of haloarcula marismortui 15 d1dbda_ 10.8 12 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 16 c2kl8A_ 10.3 22 PDB header:de novo protein Chain: A: PDB Molecule:or15; PDBTitle: solution nmr structure of de novo designed ferredoxin-like2 fold protein, northeast structural genomics consortium3 target or15 17 c2zkri_ 9.8 32 PDB header:ribosomal protein/rna Chain: I: PDB Molecule:rna expansion segment es15 part i; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 18 c1s6xA_ 9.4 36 PDB header:toxin Chain: A: PDB Molecule:kvap channel; PDBTitle: solution structure of vstx 19 c2yqrA_ 8.5 17 PDB header:rna binding protein Chain: A: PDB Molecule:kiaa0907 protein; PDBTitle: solution structure of the kh domain in kiaa0907 protein 20 c1jqmA_ 8.2 37 PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l11; PDBTitle: fitting of l11 protein and elongation factor g (ef-g) in2 the cryo-em map of e. coli 70s ribosome bound with ef-g,3 gdp and fusidic acid 21 d1a7ge_ not modelled 7.8 16 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 22 c2vhmI_ not modelled 7.8 33 PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11; PDBTitle: structure of pdf binding helix in complex with the ribosome2 (part 1 of 4) 23 d1f9fa_ not modelled 7.7 8 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 24 c3izcn_ not modelled 7.6 24 PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein rpl14 (l14e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 25 c3bboK_ not modelled 7.6 32 PDB header:ribosome Chain: K: PDB Molecule:ribosomal protein l11; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 26 c3ai4A_ not modelled 7.3 20 PDB header:fluorescent protein, replication Chain: A: PDB Molecule:yeast enhanced green fluorescent protein, dna polymerase PDBTitle: crystal structure of yeast enhanced green fluorescent protein - mouse2 polymerase iota ubiquitin binding motif fusion protein 27 d1r8ha_ not modelled 7.1 8 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 28 d2q79a1 not modelled 7.1 15 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 29 c3lpeF_ not modelled 6.4 38 PDB header:transferase Chain: F: PDB Molecule:dna-directed rna polymerase subunit e''; PDBTitle: crystal structure of spt4/5ngn heterodimer complex from methanococcus2 jannaschii 30 d1vqoi1 not modelled 6.3 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 31 c2ko4A_ not modelled 6.3 0 PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 15; PDBTitle: complex structure of the activation domain of gcn4 bound to the2 mediator co-activator domain of gal11/med15 32 d1yvua2 not modelled 6.3 7 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:PIWI domain 33 c2hxgB_ not modelled 6.0 12 PDB header:isomerase Chain: B: PDB Molecule:l-arabinose isomerase; PDBTitle: crystal structure of mn2+ bound ecai 34 d1iwga2 not modelled 5.8 15 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 35 d1vqoe2 not modelled 5.4 17 Fold:Ribosomal protein L6 Superfamily:Ribosomal protein L6 Family:Ribosomal protein L6 36 c4a1eE_ not modelled 5.4 21 PDB header:ribosome Chain: E: PDB Molecule:60s ribosomal protein l9; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1

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