Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	T	K	A	L	S	V	V	L	L	T	C	A	L	F	S	G	Q	L	M	A	G	H	K	G	H	E	F	V	W	V	K	N	V	D	H	Q	L	R	H	E	A	D	S	D	E	L	R	A	V	A	E	E	S	A	E	G	L	R
Secondary structure
SS confidence
Disorder		?	?	?																			?																		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.
Sequence		E	H	F	Y	W	Q	K	S	R	K	P	E	A	G	Q	R
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 3bbo chain F Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 28.1% Identity: 20% PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein l3; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2gyc chain B domain 1 Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 26.0% Identity: 45% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Ribosomal protein L3 Phyre2 PDB 2zjr chain B domain 1 Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 22.4% Identity: 50% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Ribosomal protein L3 Phyre2 PDB 2j01 chain E domain 1 Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 20.4% Identity: 50% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Ribosomal protein L3 Phyre2 PDB 2yqk chain A Region: 55 - 74 Aligned: 20 Modelled: 20 Confidence: 19.7% Identity: 35% PDB header:transcription/apoptosis Chain: A: PDB Molecule:arginine-glutamic acid dipeptide repeats protein; PDBTitle: solution structure of the sant domain in arginine-glutamic2 acid dipeptide (re) repeats Phyre2 PDB 2ftc chain C Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 16.7% Identity: 20% PDB header:ribosome Chain: C: PDB Molecule:mitochondrial 39s ribosomal protein l3; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome Phyre2 PDB 1vqo chain B domain 1 Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 16.2% Identity: 20% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Ribosomal protein L3 Phyre2 PDB 3jyw chain C Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 15.2% Identity: 20% PDB header:ribosome Chain: C: PDB Molecule:60s ribosomal protein l3; PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution Phyre2 PDB 1s1i chain C Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 12.6% Identity: 20% PDB header:ribosome Chain: C: PDB Molecule:60s ribosomal protein l3; 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 2zkr chain B Region: 16 - 35 Aligned: 20 Modelled: 20 Confidence: 10.5% Identity: 25% PDB header:ribosomal protein/rna Chain: B: PDB Molecule:rna expansion segment es4; 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 2kwz chain A Region: 8 - 15 Aligned: 8 Modelled: 8 Confidence: 10.4% Identity: 75% PDB header:viral protein Chain: A: PDB Molecule:protease ns2-3; PDBTitle: solution structure of ns2 [60-99] Phyre2 PDB 1ni5 chain A Region: 7 - 50 Aligned: 40 Modelled: 44 Confidence: 6.8% Identity: 28% PDB header:cell cycle Chain: A: PDB Molecule:putative cell cycle protein mesj; PDBTitle: structure of the mesj pp-atpase from escherichia coli Phyre2 PDB 3du6 chain A Region: 19 - 64 Aligned: 46 Modelled: 46 Confidence: 6.5% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: structure of the catalytic subunit of telomerase, tert Phyre2 PDB 1odp chain A Region: 45 - 61 Aligned: 17 Modelled: 17 Confidence: 5.9% Identity: 47% PDB header:lipid transport Chain: A: PDB Molecule:apoa-i peptide; PDBTitle: peptide of human apoa-i residues 166-185. nmr, 5 structures2 at ph 6.6, 37 degrees celsius and peptide:sds mole ratio3 of 1:40 Phyre2 PDB 1odq chain A Region: 45 - 61 Aligned: 17 Modelled: 17 Confidence: 5.9% Identity: 47% PDB header:lipid transport Chain: A: PDB Molecule:apoa-i peptide; PDBTitle: peptide of human apoa-i residues 166-185. nmr, 5 structures2 at ph 3.7, 37 degrees celsius and peptide:sds mole ratio3 of 1:40 Phyre2 PDB 1odr chain A Region: 45 - 61 Aligned: 17 Modelled: 17 Confidence: 5.9% Identity: 47% PDB header:lipid transport Chain: A: PDB Molecule:apoa-i peptide; PDBTitle: peptide of human apoa-i residues 166-185. nmr, 5 structures2 at ph 6.0, 37 degrees celsius and peptide:dpc mole ratio3 of 1:40 Phyre2 PDB 3mtu chain D Region: 52 - 72 Aligned: 21 Modelled: 21 Confidence: 5.8% Identity: 38% PDB header:contractile protein Chain: D: PDB Molecule:tropomyosin alpha-1 chain, microtubule-associated protein PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle Phyre2 PDB 2lci chain A Region: 32 - 57 Aligned: 26 Modelled: 26 Confidence: 5.6% Identity: 42% PDB header:de novo protein Chain: A: PDB Molecule:protein or36; PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or36 (casd3 target) Phyre2 PDB 3fd9 chain C Region: 61 - 66 Aligned: 6 Modelled: 6 Confidence: 5.6% Identity: 83% PDB header:unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the transcriptional anti-activator exsd2 from pseudomonas aeruginosa Phyre2 1 c3bboF_ 2 d2gycb1 3 d2zjrb1 4 d2j01e1 5 c2yqkA_ 6 c2ftcC_ 7 d1vqob1 8 c3jywC_ 9 c1s1iC_ 10 c2zkrb_ 11 c2kwzA_ 12 c1ni5A_ 13 c3du6A_ 14 c1odpA_ 15 c1odqA_ 16 c1odrA_ 17 c3mtuD_ 18 c2lciA_ 19 c3fd9C_

Detailed template information

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

1 c3bboF_ 28.1 20 PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein l3; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 2 d2gycb1 26.0 45 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Ribosomal protein L3 3 d2zjrb1 22.4 50 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Ribosomal protein L3 4 d2j01e1 20.4 50 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Ribosomal protein L3 5 c2yqkA_ 19.7 35 PDB header:transcription/apoptosis Chain: A: PDB Molecule:arginine-glutamic acid dipeptide repeats protein; PDBTitle: solution structure of the sant domain in arginine-glutamic2 acid dipeptide (re) repeats 6 c2ftcC_ 16.7 20 PDB header:ribosome Chain: C: PDB Molecule:mitochondrial 39s ribosomal protein l3; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome 7 d1vqob1 16.2 20 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Ribosomal protein L3 8 c3jywC_ 15.2 20 PDB header:ribosome Chain: C: PDB Molecule:60s ribosomal protein l3; PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution 9 c1s1iC_ 12.6 20 PDB header:ribosome Chain: C: PDB Molecule:60s ribosomal protein l3; 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. 10 c2zkrb_ 10.5 25 PDB header:ribosomal protein/rna Chain: B: PDB Molecule:rna expansion segment es4; 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 11 c2kwzA_ 10.4 75 PDB header:viral protein Chain: A: PDB Molecule:protease ns2-3; PDBTitle: solution structure of ns2 [60-99] 12 c1ni5A_ 6.8 28 PDB header:cell cycle Chain: A: PDB Molecule:putative cell cycle protein mesj; PDBTitle: structure of the mesj pp-atpase from escherichia coli 13 c3du6A_ 6.5 15 PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: structure of the catalytic subunit of telomerase, tert 14 c1odpA_ 5.9 47 PDB header:lipid transport Chain: A: PDB Molecule:apoa-i peptide; PDBTitle: peptide of human apoa-i residues 166-185. nmr, 5 structures2 at ph 6.6, 37 degrees celsius and peptide:sds mole ratio3 of 1:40 15 c1odqA_ 5.9 47 PDB header:lipid transport Chain: A: PDB Molecule:apoa-i peptide; PDBTitle: peptide of human apoa-i residues 166-185. nmr, 5 structures2 at ph 3.7, 37 degrees celsius and peptide:sds mole ratio3 of 1:40 16 c1odrA_ 5.9 47 PDB header:lipid transport Chain: A: PDB Molecule:apoa-i peptide; PDBTitle: peptide of human apoa-i residues 166-185. nmr, 5 structures2 at ph 6.0, 37 degrees celsius and peptide:dpc mole ratio3 of 1:40 17 c3mtuD_ 5.8 38 PDB header:contractile protein Chain: D: PDB Molecule:tropomyosin alpha-1 chain, microtubule-associated protein PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle 18 c2lciA_ 5.6 42 PDB header:de novo protein Chain: A: PDB Molecule:protein or36; PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or36 (casd3 target) 19 c3fd9C_ 5.6 83 PDB header:unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the transcriptional anti-activator exsd2 from pseudomonas aeruginosa

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