Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	H	K	K	A	G	G	S	T	R	N	G	R	D	S	E	A	K	R	L	G	V	K	R	F	G	G	E	S	V	L	A	G	S	I	I	V	R	Q	R	G	T	K	F	H	A	G	A	N	V	G	C	G	R	D	H	T	L	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.
Sequence		A	K	A	D	G	K	V	K	F	E	V	K	G	P	K	N	R	K	F	I	S	I	E	A	E
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 3fin chain 0 Region: 1 - 85 Aligned: 84 Modelled: 85 Confidence: 100.0% Identity: 60% PDB header:ribosome Chain: 0: PDB Molecule:50s ribosomal protein l27; PDBTitle: t. thermophilus 70s ribosome in complex with mrna, trnas2 and ef-tu.gdp.kirromycin ternary complex, fitted to a 6.43 a cryo-em map. this file contains the 50s subunit. Phyre2 PDB 2gyc chain U domain 1 Region: 2 - 85 Aligned: 84 Modelled: 84 Confidence: 100.0% Identity: 100% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: Ribosomal L27 protein Phyre2 PDB 2zjr chain T domain 1 Region: 2 - 84 Aligned: 82 Modelled: 83 Confidence: 100.0% Identity: 71% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: Ribosomal L27 protein Phyre2 PDB 3bbo chain X Region: 2 - 85 Aligned: 83 Modelled: 83 Confidence: 100.0% Identity: 61% PDB header:ribosome Chain: X: PDB Molecule:ribosomal protein l27; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2ftc chain O Region: 2 - 69 Aligned: 68 Modelled: 68 Confidence: 100.0% Identity: 44% PDB header:ribosome Chain: O: PDB Molecule:mitochondrial 39s ribosomal protein l27; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome Phyre2 PDB 1v8q chain A Region: 20 - 85 Aligned: 65 Modelled: 66 Confidence: 100.0% Identity: 52% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: Ribosomal L27 protein Phyre2 PDB 2ba0 chain A domain 2 Region: 29 - 84 Aligned: 46 Modelled: 56 Confidence: 94.0% Identity: 17% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: ECR1 N-terminal domain-like Phyre2 PDB 2je6 chain I domain 2 Region: 29 - 84 Aligned: 47 Modelled: 56 Confidence: 93.0% Identity: 9% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: ECR1 N-terminal domain-like Phyre2 PDB 2nn6 chain H domain 2 Region: 29 - 84 Aligned: 47 Modelled: 56 Confidence: 91.5% Identity: 32% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: ECR1 N-terminal domain-like Phyre2 PDB 2ba1 chain B Region: 29 - 84 Aligned: 47 Modelled: 56 Confidence: 86.2% Identity: 26% PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core Phyre2 PDB 2nn6 chain H Region: 29 - 84 Aligned: 47 Modelled: 56 Confidence: 86.0% Identity: 32% PDB header:hydrolase/transferase Chain: H: PDB Molecule:exosome complex exonuclease rrp4; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 Phyre2 PDB 2nn6 chain I domain 2 Region: 30 - 85 Aligned: 52 Modelled: 56 Confidence: 83.6% Identity: 13% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: ECR1 N-terminal domain-like Phyre2 PDB 2nn6 chain G Region: 26 - 84 Aligned: 58 Modelled: 59 Confidence: 82.5% Identity: 16% PDB header:hydrolase/transferase Chain: G: PDB Molecule:exosome complex exonuclease rrp40; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 Phyre2 PDB 2nn6 chain I Region: 30 - 85 Aligned: 52 Modelled: 56 Confidence: 80.0% Identity: 13% PDB header:hydrolase/transferase Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 Phyre2 PDB 2ba0 chain A Region: 29 - 84 Aligned: 46 Modelled: 56 Confidence: 67.1% Identity: 17% PDB header:rna binding protein Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4; PDBTitle: archaeal exosome core Phyre2 PDB 2auk chain A Region: 27 - 70 Aligned: 32 Modelled: 44 Confidence: 36.3% Identity: 22% PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase beta' chain; PDBTitle: structure of e. coli rna polymerase beta' g/g' insert Phyre2 PDB 2yyo chain A Region: 42 - 85 Aligned: 40 Modelled: 43 Confidence: 35.0% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:spry domain-containing protein 3; PDBTitle: crystal sturcture of human spry domain Phyre2 PDB 2b44 chain A Region: 33 - 69 Aligned: 37 Modelled: 37 Confidence: 34.4% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:glycyl-glycine endopeptidase lytm; PDBTitle: truncated s. aureus lytm, p 32 2 1 crystal form Phyre2 PDB 1qwy chain A Region: 41 - 69 Aligned: 29 Modelled: 29 Confidence: 34.0% Identity: 21% Fold: Barrel-sandwich hybrid Superfamily: Duplicated hybrid motif Family: Peptidoglycan hydrolase LytM Phyre2 PDB 1eyb chain A Region: 26 - 63 Aligned: 34 Modelled: 38 Confidence: 26.1% Identity: 26% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Homogentisate dioxygenase Phyre2 1 c3fin0_ 2 d2gycu1 3 d2zjrt1 4 c3bboX_ 5 c2ftcO_ 6 d1v8qa_ 7 d2ba0a2 8 d2je6i2 9 d2nn6h2 10 c2ba1B_ 11 c2nn6H_ 12 d2nn6i2 13 c2nn6G_ 14 c2nn6I_ 15 c2ba0A_ 16 c2aukA_ 17 c2yyoA_ 18 c2b44A_ 19 d1qwya_ 20 d1eyba_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

Detailed template information

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

1 c3fin0_ 100.0 60 PDB header:ribosome Chain: 0: PDB Molecule:50s ribosomal protein l27; PDBTitle: t. thermophilus 70s ribosome in complex with mrna, trnas2 and ef-tu.gdp.kirromycin ternary complex, fitted to a 6.43 a cryo-em map. this file contains the 50s subunit. 2 d2gycu1 100.0 100 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:Ribosomal L27 protein 3 d2zjrt1 100.0 71 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:Ribosomal L27 protein 4 c3bboX_ 100.0 61 PDB header:ribosome Chain: X: PDB Molecule:ribosomal protein l27; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 5 c2ftcO_ 100.0 44 PDB header:ribosome Chain: O: PDB Molecule:mitochondrial 39s ribosomal protein l27; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome 6 d1v8qa_ 100.0 52 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:Ribosomal L27 protein 7 d2ba0a2 94.0 17 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 8 d2je6i2 93.0 9 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 9 d2nn6h2 91.5 32 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 10 c2ba1B_ 86.2 26 PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core 11 c2nn6H_ 86.0 32 PDB header:hydrolase/transferase Chain: H: PDB Molecule:exosome complex exonuclease rrp4; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 12 d2nn6i2 83.6 13 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 13 c2nn6G_ 82.5 16 PDB header:hydrolase/transferase Chain: G: PDB Molecule:exosome complex exonuclease rrp40; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 14 c2nn6I_ 80.0 13 PDB header:hydrolase/transferase Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 15 c2ba0A_ 67.1 17 PDB header:rna binding protein Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4; PDBTitle: archaeal exosome core 16 c2aukA_ 36.3 22 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase beta' chain; PDBTitle: structure of e. coli rna polymerase beta' g/g' insert 17 c2yyoA_ 35.0 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:spry domain-containing protein 3; PDBTitle: crystal sturcture of human spry domain 18 c2b44A_ 34.4 19 PDB header:hydrolase Chain: A: PDB Molecule:glycyl-glycine endopeptidase lytm; PDBTitle: truncated s. aureus lytm, p 32 2 1 crystal form 19 d1qwya_ 34.0 21 Fold:Barrel-sandwich hybrid Superfamily:Duplicated hybrid motif Family:Peptidoglycan hydrolase LytM 20 d1eyba_ 26.1 26 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Homogentisate dioxygenase 21 c1ey2A_ not modelled 26.1 26 PDB header:oxidoreductase Chain: A: PDB Molecule:homogentisate 1,2-dioxygenase; PDBTitle: human homogentisate dioxygenase with fe(ii) 22 c3c8vA_ not modelled 19.2 26 PDB header:transferase Chain: A: PDB Molecule:putative acetyltransferase; PDBTitle: crystal structure of putative acetyltransferase (yp_390128.1) from2 desulfovibrio desulfuricans g20 at 2.28 a resolution 23 c2jz2A_ not modelled 15.0 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ssl0352 protein; PDBTitle: solution nmr structure of ssl0352 protein from synechocystis sp. pcc2 6803. northeast structural genomics consortium target sgr42 24 c2cupA_ not modelled 11.3 30 PDB header:metal binding protein Chain: A: PDB Molecule:skeletal muscle lim-protein 1; PDBTitle: solution structure of the skeletal muscle lim-protein 1 25 d1qpoa2 not modelled 9.8 15 Fold:alpha/beta-Hammerhead Superfamily:Nicotinate/Quinolinate PRTase N-terminal domain-like Family:NadC N-terminal domain-like 26 c2dn8A_ not modelled 9.8 30 PDB header:ligase Chain: A: PDB Molecule:acetyl-coa carboxylase 2; PDBTitle: solution structure of rsgi ruh-053, an apo-biotin carboxy2 carrier protein from human transcarboxylase 27 d2incc1 not modelled 9.1 27 Fold:beta-Grasp (ubiquitin-like) Superfamily:TmoB-like Family:TmoB-like 28 d2fsqa1 not modelled 9.0 23 Fold:LigT-like Superfamily:LigT-like Family:Atu0111-like 29 c2je6I_ not modelled 8.4 6 PDB header:hydrolase Chain: I: PDB Molecule:exosome complex rna-binding protein 1; PDBTitle: structure of a 9-subunit archaeal exosome 30 c2kytA_ not modelled 8.2 29 PDB header:hydrolase Chain: A: PDB Molecule:group xvi phospholipase a2; PDBTitle: solution struture of the h-rev107 n-terminal domain 31 d1a6ca3 not modelled 8.1 26 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 32 d1o4ua2 not modelled 8.0 20 Fold:alpha/beta-Hammerhead Superfamily:Nicotinate/Quinolinate PRTase N-terminal domain-like Family:NadC N-terminal domain-like 33 d1x3ha1 not modelled 7.2 14 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 34 c3lazB_ not modelled 6.1 42 PDB header:lyase Chain: B: PDB Molecule:d-galactarate dehydratase; PDBTitle: the crystal structure of the n-terminal domain of d-2 galactarate dehydratase from escherichia coli cft073 35 c3tbiB_ not modelled 6.0 45 PDB header:transcription Chain: B: PDB Molecule:dna-directed rna polymerase subunit beta; PDBTitle: crystal structure of t4 gp33 bound to e. coli rnap beta-flap domain 36 c3nyyA_ not modelled 5.9 22 PDB header:hydrolase Chain: A: PDB Molecule:putative glycyl-glycine endopeptidase lytm; PDBTitle: crystal structure of a putative glycyl-glycine endopeptidase lytm2 (rumgna_02482) from ruminococcus gnavus atcc 29149 at 1.60 a3 resolution 37 c2l1sA_ not modelled 5.7 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yohn; PDBTitle: yp_001336205.1 38 c3h41A_ not modelled 5.7 20 PDB header:hydrolase Chain: A: PDB Molecule:nlp/p60 family protein; PDBTitle: crystal structure of a nlpc/p60 family protein (bce_2878) from2 bacillus cereus atcc 10987 at 1.79 a resolution 39 d1qapa2 not modelled 5.6 19 Fold:alpha/beta-Hammerhead Superfamily:Nicotinate/Quinolinate PRTase N-terminal domain-like Family:NadC N-terminal domain-like 40 c3es1A_ not modelled 5.5 36 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of protein with a cupin-like fold and unknown2 function (yp_001165807.1) from novosphingobium aromaticivorans dsm3 12444 at 1.91 a resolution 41 d1ne9a1 not modelled 5.3 13 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:FemXAB nonribosomal peptidyltransferases

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