Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	Q	S	M	K	A	R	E	V	K	R	V	A	L	A	D	K	Y	F	A	K	R	A	E	L	K	A	I	I	S	D	V	N	A	S	D	E	D	R	W	N	A	V	L	K	L	Q	T	L	P	R	D	S	S	P	S	R	Q
Secondary structure
SS confidence
Disorder		?	?	?																													?		?		?	?															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.
Sequence		R	N	R	C	R	Q	T	G	R	P	H	G	F	L	R	K	F	G	L	S	R	I	K	V	R	E	A	A	M	R	G	E	I	P	G	L	K	K	A	S	W
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 N domain 1 Region: 2 - 101 Aligned: 96 Modelled: 100 Confidence: 100.0% Identity: 100% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: Ribosomal protein S14 Phyre2 PDB 3bbn chain N Region: 2 - 101 Aligned: 99 Modelled: 100 Confidence: 100.0% Identity: 40% PDB header:ribosome Chain: N: PDB Molecule:ribosomal protein s14; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 2gy9 chain N Region: 41 - 101 Aligned: 61 Modelled: 61 Confidence: 99.9% Identity: 100% PDB header:ribosome Chain: N: PDB Molecule:30s ribosomal subunit protein s14; PDBTitle: structure of the 30s subunit of a pre-translocational e.2 coli ribosome obtained by fitting atomic models for rna and3 protein components into cryo-em map emd-1056 Phyre2 PDB 2uub chain N domain 1 Region: 48 - 101 Aligned: 54 Modelled: 54 Confidence: 99.9% Identity: 41% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: Ribosomal protein S14 Phyre2 PDB 3jyv chain N Region: 62 - 89 Aligned: 28 Modelled: 28 Confidence: 93.8% Identity: 32% PDB header:ribosome Chain: N: PDB Molecule:40s ribosomal protein s29(a); PDBTitle: structure of the 40s rrna and proteins and p/e trna for eukaryotic2 ribosome based on cryo-em map of thermomyces lanuginosus ribosome at3 8.9a resolution Phyre2 PDB 2xzn chain N Region: 62 - 89 Aligned: 28 Modelled: 28 Confidence: 93.7% Identity: 32% PDB header:ribosome Chain: N: PDB Molecule:rps29e; 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 N Region: 62 - 88 Aligned: 27 Modelled: 27 Confidence: 91.8% Identity: 33% PDB header:ribosomal protein/rna Chain: N: 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 N Region: 64 - 89 Aligned: 26 Modelled: 26 Confidence: 75.3% Identity: 35% PDB header:ribosome Chain: N: PDB Molecule:40s ribosomal protein s29-b; 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 2bmf chain A domain 1 Region: 72 - 94 Aligned: 23 Modelled: 23 Confidence: 21.0% Identity: 30% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RNA helicase Phyre2 PDB 2zhh chain A Region: 75 - 100 Aligned: 26 Modelled: 26 Confidence: 20.1% Identity: 12% PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr Phyre2 PDB 1r8d chain A Region: 75 - 100 Aligned: 26 Modelled: 26 Confidence: 14.5% Identity: 8% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: DNA-binding N-terminal domain of transcription activators Phyre2 PDB 2iea chain A domain 3 Region: 66 - 94 Aligned: 29 Modelled: 29 Confidence: 13.4% Identity: 24% Fold: TK C-terminal domain-like Superfamily: TK C-terminal domain-like Family: Transketolase C-terminal domain-like Phyre2 PDB 3gpv chain A Region: 75 - 100 Aligned: 26 Modelled: 24 Confidence: 13.0% Identity: 19% PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis Phyre2 PDB 1qw1 chain A Region: 72 - 97 Aligned: 26 Modelled: 26 Confidence: 12.9% Identity: 12% PDB header:gene regulation Chain: A: PDB Molecule:diphtheria toxin repressor; PDBTitle: solution structure of the c-terminal domain of dtxr2 residues 110-226 Phyre2 PDB 1yuz chain B Region: 64 - 77 Aligned: 14 Modelled: 14 Confidence: 12.3% Identity: 21% PDB header:oxidoreductase Chain: B: PDB Molecule:nigerythrin; PDBTitle: partially reduced state of nigerythrin Phyre2 PDB 3izb chain V Region: 78 - 100 Aligned: 23 Modelled: 23 Confidence: 11.0% Identity: 35% PDB header:ribosome Chain: V: PDB Molecule:40s ribosomal protein rps25 (s25e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 1y6u chain A Region: 77 - 91 Aligned: 15 Modelled: 15 Confidence: 10.3% Identity: 27% 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 Phyre2 PDB 2xzm chain 8 Region: 79 - 100 Aligned: 22 Modelled: 22 Confidence: 9.9% Identity: 27% PDB header:ribosome Chain: 8: PDB Molecule:rps25e,; 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 2cp5 chain A domain 1 Region: 59 - 78 Aligned: 20 Modelled: 20 Confidence: 9.8% Identity: 30% Fold: SH3-like barrel Superfamily: Cap-Gly domain Family: Cap-Gly domain Phyre2 PDB 3iz6 chain V Region: 78 - 100 Aligned: 23 Modelled: 23 Confidence: 9.1% Identity: 26% PDB header:ribosome Chain: V: PDB Molecule:40s ribosomal protein s25 (s25e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 1 d2qaln1 2 c3bbnN_ 3 c2gy9N_ 4 d2uubn1 5 c3jyvN_ 6 c2xznN_ 7 c2zkqn_ 8 c1s1hN_ 9 d2bmfa1 10 c2zhhA_ 11 d1r8da_ 12 d2ieaa3 13 c3gpvA_ 14 c1qw1A_ 15 c1yuzB_ 16 c3izbV_ 17 c1y6uA_ 18 c2xzm8_ 19 d2cp5a1 20 c3iz6V_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 d2qaln1 100.0 100 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Ribosomal protein S14 2 c3bbnN_ 100.0 40 PDB header:ribosome Chain: N: PDB Molecule:ribosomal protein s14; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 3 c2gy9N_ 99.9 100 PDB header:ribosome Chain: N: PDB Molecule:30s ribosomal subunit protein s14; PDBTitle: structure of the 30s subunit of a pre-translocational e.2 coli ribosome obtained by fitting atomic models for rna and3 protein components into cryo-em map emd-1056 4 d2uubn1 99.9 41 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Ribosomal protein S14 5 c3jyvN_ 93.8 32 PDB header:ribosome Chain: N: PDB Molecule:40s ribosomal protein s29(a); PDBTitle: structure of the 40s rrna and proteins and p/e trna for eukaryotic2 ribosome based on cryo-em map of thermomyces lanuginosus ribosome at3 8.9a resolution 6 c2xznN_ 93.7 32 PDB header:ribosome Chain: N: PDB Molecule:rps29e; 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 7 c2zkqn_ 91.8 33 PDB header:ribosomal protein/rna Chain: N: 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 8 c1s1hN_ 75.3 35 PDB header:ribosome Chain: N: PDB Molecule:40s ribosomal protein s29-b; 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. 9 d2bmfa1 21.0 30 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RNA helicase 10 c2zhhA_ 20.1 12 PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr 11 d1r8da_ 14.5 8 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 12 d2ieaa3 13.4 24 Fold:TK C-terminal domain-like Superfamily:TK C-terminal domain-like Family:Transketolase C-terminal domain-like 13 c3gpvA_ 13.0 19 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis 14 c1qw1A_ 12.9 12 PDB header:gene regulation Chain: A: PDB Molecule:diphtheria toxin repressor; PDBTitle: solution structure of the c-terminal domain of dtxr2 residues 110-226 15 c1yuzB_ 12.3 21 PDB header:oxidoreductase Chain: B: PDB Molecule:nigerythrin; PDBTitle: partially reduced state of nigerythrin 16 c3izbV_ 11.0 35 PDB header:ribosome Chain: V: PDB Molecule:40s ribosomal protein rps25 (s25e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 17 c1y6uA_ 10.3 27 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 18 c2xzm8_ 9.9 27 PDB header:ribosome Chain: 8: PDB Molecule:rps25e,; 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 19 d2cp5a1 9.8 30 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 20 c3iz6V_ 9.1 26 PDB header:ribosome Chain: V: PDB Molecule:40s ribosomal protein s25 (s25e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 21 d1n10a2 not modelled 8.7 17 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:Pollen allergen PHL P 1 N-terminal domain 22 d1nj1a2 not modelled 8.7 17 Fold:IF3-like Superfamily:C-terminal domain of ProRS Family:C-terminal domain of ProRS 23 c3bboY_ not modelled 7.8 38 PDB header:ribosome Chain: Y: PDB Molecule:ribosomal protein l28; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 24 d1kcfa1 not modelled 7.4 25 Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain 25 c1z4hA_ not modelled 7.3 14 PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:tor inhibition protein; PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase 26 c2fugC_ not modelled 7.1 38 PDB header:oxidoreductase Chain: C: PDB Molecule:nadh-quinone oxidoreductase chain 3; PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus 27 d2qamz1 not modelled 6.8 38 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L28 28 d1e0ea_ not modelled 6.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:N-terminal Zn binding domain of HIV integrase Family:N-terminal Zn binding domain of HIV integrase 29 d1s7za_ not modelled 6.4 33 Fold:Another 3-helical bundle Superfamily:B-form DNA mimic Ocr Family:B-form DNA mimic Ocr 30 c3hh0C_ not modelled 6.3 4 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus 31 d1whha_ not modelled 6.2 17 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 32 d1wg2a_ not modelled 5.9 28 Fold:AN1-like Zinc finger Superfamily:AN1-like Zinc finger Family:AN1-like Zinc finger 33 d1whja_ not modelled 5.5 30 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 34 d1k6ya1 not modelled 5.4 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:N-terminal Zn binding domain of HIV integrase Family:N-terminal Zn binding domain of HIV integrase 35 d2coza1 not modelled 5.4 25 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 36 c2k0aA_ not modelled 5.3 21 PDB header:metal binding protein Chain: A: PDB Molecule:pre-mrna-splicing factor rds3; PDBTitle: 1h, 15n and 13c chemical shift assignments for rds3 protein 37 d1wjfa_ not modelled 5.2 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:N-terminal Zn binding domain of HIV integrase Family:N-terminal Zn binding domain of HIV integrase 38 d2coya1 not modelled 5.2 21 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain

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