Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	V	A	Y	I	A	I	G	S	N	L	A	S	P	L	E	Q	V	N	A	A	L	K	A	L	G	D	I	P	E	S	H	I	L	T	V	S	S	F	Y	R	T	P	P	L	G	P	Q	D	Q	P	D	Y	L	N	A	A	V	A
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	E	T	S	L	A	P	E	E	L	L	N	H	T	Q	R	I	E	L	Q	Q	G	R	V	R	K	A	E	R	W	G	P	R	T	L	D	L	D	I	M	L	F	G	N	E	V	I	N	T	E	R	L	T	V	P	H	Y	D	M	K
Secondary structure
SS confidence
Disorder																							?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.
Sequence		N	R	G	F	M	L	W	P	L	F	E	I	A	P	E	L	V	F	P	D	G	E	M	L	R	Q	I	L	H	T	R	A	F	D	K	L	N	K	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 1f9y chain A Region: 2 - 159 Aligned: 158 Modelled: 158 Confidence: 100.0% Identity: 100% Fold: Ferredoxin-like Superfamily: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK Family: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK Phyre2 PDB 1cbk chain A Region: 1 - 158 Aligned: 157 Modelled: 158 Confidence: 100.0% Identity: 57% Fold: Ferredoxin-like Superfamily: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK Family: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK Phyre2 PDB 2qx0 chain A Region: 1 - 159 Aligned: 158 Modelled: 159 Confidence: 100.0% Identity: 63% PDB header:transferase Chain: A: PDB Molecule:7,8-dihydro-6-hydroxymethylpterin- PDBTitle: crystal structure of yersinia pestis hppk (ternary complex) Phyre2 PDB 2bmb chain A Region: 2 - 154 Aligned: 144 Modelled: 153 Confidence: 100.0% Identity: 33% PDB header:transferase Chain: A: PDB Molecule:folic acid synthesis protein fol1; PDBTitle: x-ray structure of the bifunctional 6-hydroxymethyl-7,8-2 dihydroxypterin pyrophosphokinase dihydropteroate synthase3 from saccharomyces cerevisiae Phyre2 PDB 3mcn chain A Region: 1 - 152 Aligned: 139 Modelled: 152 Confidence: 100.0% Identity: 36% PDB header:transferase Chain: A: PDB Molecule:2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PDBTitle: crystal structure of the 6-hyroxymethyl-7,8-dihydropterin2 pyrophosphokinase dihydropteroate synthase bifunctional enzyme from3 francisella tularensis Phyre2 PDB 2cg8 chain B Region: 2 - 150 Aligned: 131 Modelled: 140 Confidence: 100.0% Identity: 34% PDB header:lyase/transferase Chain: B: PDB Molecule:dihydroneopterin aldolase 6-hydroxymethyl-7,8- PDBTitle: the bifunctional dihydroneopterin aldolase 6-hydroxymethyl-2 7,8-dihydropterin synthase from streptococcus pneumoniae Phyre2 PDB 3r3t chain A Region: 55 - 95 Aligned: 41 Modelled: 41 Confidence: 31.1% Identity: 15% PDB header:rna binding protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s from bacillus anthracis Phyre2 PDB 2j5a chain A domain 1 Region: 53 - 95 Aligned: 43 Modelled: 43 Confidence: 28.1% Identity: 28% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 2o6l chain A Region: 2 - 37 Aligned: 36 Modelled: 36 Confidence: 24.9% Identity: 25% PDB header:transferase Chain: A: PDB Molecule:udp-glucuronosyltransferase 2b7; PDBTitle: crystal structure of the udp-glucuronic acid binding domain2 of the human drug metabolizing udp-glucuronosyltransferase3 2b7 Phyre2 PDB 3ndc chain B Region: 1 - 28 Aligned: 26 Modelled: 28 Confidence: 23.0% Identity: 19% PDB header:transferase Chain: B: PDB Molecule:precorrin-4 c(11)-methyltransferase; PDBTitle: crystal structure of precorrin-4 c11-methyltransferase from2 rhodobacter capsulatus Phyre2 PDB 1qjh chain A Region: 53 - 95 Aligned: 43 Modelled: 43 Confidence: 22.8% Identity: 23% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 1lou chain A Region: 53 - 95 Aligned: 43 Modelled: 43 Confidence: 20.0% Identity: 26% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 3bbn chain F Region: 53 - 95 Aligned: 43 Modelled: 43 Confidence: 15.0% Identity: 19% PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein s6; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 3idw chain A Region: 69 - 83 Aligned: 15 Modelled: 15 Confidence: 13.7% Identity: 13% PDB header:endocytosis Chain: A: PDB Molecule:actin cytoskeleton-regulatory complex protein sla1; PDBTitle: crystal structure of sla1 homology domain 2 Phyre2 PDB 2inp chain D Region: 76 - 97 Aligned: 21 Modelled: 22 Confidence: 13.4% Identity: 19% PDB header:oxidoreductase Chain: D: PDB Molecule:phenol hydroxylase component phl; PDBTitle: structure of the phenol hydroxylase-regulatory protein2 complex Phyre2 PDB 1t6c chain A domain 1 Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 12.3% Identity: 64% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Ppx/GppA phosphatase Phyre2 PDB 1vmb chain A Region: 55 - 95 Aligned: 41 Modelled: 41 Confidence: 12.3% Identity: 24% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 1vmb chain A Region: 55 - 95 Aligned: 41 Modelled: 41 Confidence: 12.3% Identity: 24% PDB header:translation Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s6 (tm0603) from thermotoga2 maritima at 1.70 a resolution Phyre2 PDB 2bcg chain G domain 3 Region: 4 - 42 Aligned: 38 Modelled: 39 Confidence: 11.8% Identity: 29% Fold: FAD-linked reductases, C-terminal domain Superfamily: FAD-linked reductases, C-terminal domain Family: GDI-like Phyre2 PDB 1d5t chain A domain 2 Region: 4 - 42 Aligned: 38 Modelled: 39 Confidence: 10.9% Identity: 34% Fold: FAD-linked reductases, C-terminal domain Superfamily: FAD-linked reductases, C-terminal domain Family: GDI-like Phyre2 1 d1f9ya_ 2 d1cbka_ 3 c2qx0A_ 4 c2bmbA_ 5 c3mcnA_ 6 c2cg8B_ 7 c3r3tA_ 8 d2j5aa1 9 c2o6lA_ 10 c3ndcB_ 11 d1qjha_ 12 d1loua_ 13 c3bbnF_ 14 c3idwA_ 15 c2inpD_ 16 d1t6ca1 17 d1vmba_ 18 c1vmbA_ 19 d2bcgg3 20 d1d5ta2 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62

Detailed template information

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

1 d1f9ya_ 100.0 100 Fold:Ferredoxin-like Superfamily:6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK Family:6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK 2 d1cbka_ 100.0 57 Fold:Ferredoxin-like Superfamily:6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK Family:6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK 3 c2qx0A_ 100.0 63 PDB header:transferase Chain: A: PDB Molecule:7,8-dihydro-6-hydroxymethylpterin- PDBTitle: crystal structure of yersinia pestis hppk (ternary complex) 4 c2bmbA_ 100.0 33 PDB header:transferase Chain: A: PDB Molecule:folic acid synthesis protein fol1; PDBTitle: x-ray structure of the bifunctional 6-hydroxymethyl-7,8-2 dihydroxypterin pyrophosphokinase dihydropteroate synthase3 from saccharomyces cerevisiae 5 c3mcnA_ 100.0 36 PDB header:transferase Chain: A: PDB Molecule:2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PDBTitle: crystal structure of the 6-hyroxymethyl-7,8-dihydropterin2 pyrophosphokinase dihydropteroate synthase bifunctional enzyme from3 francisella tularensis 6 c2cg8B_ 100.0 34 PDB header:lyase/transferase Chain: B: PDB Molecule:dihydroneopterin aldolase 6-hydroxymethyl-7,8- PDBTitle: the bifunctional dihydroneopterin aldolase 6-hydroxymethyl-2 7,8-dihydropterin synthase from streptococcus pneumoniae 7 c3r3tA_ 31.1 15 PDB header:rna binding protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s from bacillus anthracis 8 d2j5aa1 28.1 28 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 9 c2o6lA_ 24.9 25 PDB header:transferase Chain: A: PDB Molecule:udp-glucuronosyltransferase 2b7; PDBTitle: crystal structure of the udp-glucuronic acid binding domain2 of the human drug metabolizing udp-glucuronosyltransferase3 2b7 10 c3ndcB_ 23.0 19 PDB header:transferase Chain: B: PDB Molecule:precorrin-4 c(11)-methyltransferase; PDBTitle: crystal structure of precorrin-4 c11-methyltransferase from2 rhodobacter capsulatus 11 d1qjha_ 22.8 23 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 12 d1loua_ 20.0 26 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 13 c3bbnF_ 15.0 19 PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein s6; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 14 c3idwA_ 13.7 13 PDB header:endocytosis Chain: A: PDB Molecule:actin cytoskeleton-regulatory complex protein sla1; PDBTitle: crystal structure of sla1 homology domain 2 15 c2inpD_ 13.4 19 PDB header:oxidoreductase Chain: D: PDB Molecule:phenol hydroxylase component phl; PDBTitle: structure of the phenol hydroxylase-regulatory protein2 complex 16 d1t6ca1 12.3 64 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Ppx/GppA phosphatase 17 d1vmba_ 12.3 24 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 18 c1vmbA_ 12.3 24 PDB header:translation Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s6 (tm0603) from thermotoga2 maritima at 1.70 a resolution 19 d2bcgg3 11.8 29 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:GDI-like 20 d1d5ta2 10.9 34 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:GDI-like 21 c1u9gA_ not modelled 10.9 37 PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: heterocyclic peptide backbone modification in gcn4-pli based coiled2 coils: replacement of k(8)l(9) 22 c2wc1A_ not modelled 10.0 15 PDB header:electron transport Chain: A: PDB Molecule:flavodoxin; PDBTitle: three-dimensional structure of the nitrogen fixation2 flavodoxin (niff) from rhodobacter capsulatus at 2.2 a 23 c1w5kD_ not modelled 9.6 32 PDB header:four helix bundle Chain: D: PDB Molecule:general control protein gcn4; PDBTitle: an anti-parallel four helix bundle 24 c1w5kC_ not modelled 9.6 32 PDB header:four helix bundle Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: an anti-parallel four helix bundle 25 c1w5kB_ not modelled 9.6 32 PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: an anti-parallel four helix bundle 26 c1w5kA_ not modelled 9.6 32 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: an anti-parallel four helix bundle 27 c1yzvA_ not modelled 9.4 7 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: hypothetical protein from trypanosoma cruzi 28 c1unyA_ not modelled 8.7 38 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 29 c1unvB_ not modelled 8.6 38 PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 30 c1unvA_ not modelled 8.5 38 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 31 c2ehbD_ not modelled 8.3 14 PDB header:signalling protein/transferase Chain: D: PDB Molecule:cbl-interacting serine/threonine-protein kinase 24; PDBTitle: the structure of the c-terminal domain of the protein kinase atsos22 bound to the calcium sensor atsos3 32 c2q4dB_ not modelled 8.2 15 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:lysine decarboxylase-like protein at5g11950; PDBTitle: ensemble refinement of the crystal structure of a lysine2 decarboxylase-like protein from arabidopsis thaliana gene at5g11950 33 c2kjwA_ not modelled 7.9 26 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 34 c1u9gB_ not modelled 7.9 38 PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: heterocyclic peptide backbone modification in gcn4-pli based coiled2 coils: replacement of k(8)l(9) 35 c2la3A_ not modelled 7.8 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the nmr structure of the protein np_344798.1 reveals a cca-adding2 enzyme head domain 36 c1unzA_ not modelled 7.5 38 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 37 c1unzB_ not modelled 7.5 38 PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 38 c3a4cA_ not modelled 7.5 33 PDB header:cell cycle, replication Chain: A: PDB Molecule:dna replication factor cdt1; PDBTitle: crystal structure of cdt1 c terminal domain 39 c2qikA_ not modelled 7.1 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0131 protein ykqa; PDBTitle: crystal structure of ykqa from bacillus subtilis. northeast2 structural genomics target sr631 40 c2qbbF_ not modelled 7.0 19 PDB header:ribosome Chain: F: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with gentamicin. this file3 contains the 30s subunit of the second 70s ribosome, with4 gentamicin bound. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. 41 d2qalf1 not modelled 7.0 19 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 42 d1dd3a1 not modelled 7.0 26 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain 43 c2zdiC_ not modelled 6.6 19 PDB header:chaperone Chain: C: PDB Molecule:prefoldin subunit alpha; PDBTitle: crystal structure of prefoldin from pyrococcus horikoshii2 ot3 44 c3s7xC_ not modelled 6.5 25 PDB header:viral protein Chain: C: PDB Molecule:major capsid protein vp1; PDBTitle: unassembled washington university polyomavirus vp1 pentamer r198k2 mutant 45 c2dboA_ not modelled 6.3 22 PDB header:hydrolase Chain: A: PDB Molecule:d-tyrosyl-trna(tyr) deacylase; PDBTitle: crystal structure of d-tyr-trna(tyr) deacylase from aquifex aeolicus 46 d1tjna_ not modelled 5.9 16 Fold:Chelatase-like Superfamily:Chelatase Family:CbiX-like 47 c1tjnA_ not modelled 5.9 16 PDB header:lyase Chain: A: PDB Molecule:sirohydrochlorin cobaltochelatase; PDBTitle: crystal structure of hypothetical protein af0721 from archaeoglobus2 fulgidus 48 c1zawV_ not modelled 5.8 26 PDB header:structural protein Chain: V: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a 49 c1zawU_ not modelled 5.8 26 PDB header:structural protein Chain: U: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a 50 c1zawW_ not modelled 5.8 26 PDB header:structural protein Chain: W: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a 51 c1zaxV_ not modelled 5.6 26 PDB header:structural protein Chain: V: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form b 52 c1zavW_ not modelled 5.6 26 PDB header:structural protein Chain: W: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p21 53 c1zaxW_ not modelled 5.6 26 PDB header:structural protein Chain: W: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form b 54 c1zavV_ not modelled 5.6 26 PDB header:structural protein Chain: V: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p21 55 d1hn0a4 not modelled 5.6 56 Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:Hyaluronate lyase-like, central domain 56 d1fxkc_ not modelled 5.6 8 Fold:Long alpha-hairpin Superfamily:Prefoldin Family:Prefoldin 57 c1dd3C_ not modelled 5.4 26 PDB header:ribosome Chain: C: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: crystal structure of ribosomal protein l12 from thermotoga maritima 58 c1dd3D_ not modelled 5.4 26 PDB header:ribosome Chain: D: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: crystal structure of ribosomal protein l12 from thermotoga maritima 59 d1dd4c_ not modelled 5.3 26 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain 60 c3g9rF_ not modelled 5.3 42 PDB header:viral protein Chain: F: PDB Molecule:fusion complex of hiv-1 envelope glycoprotein PDBTitle: structure of the hiv-1 gp41 membrane-proximal ectodomain2 region in a putative prefusion conformation 61 c2rbhA_ not modelled 5.3 38 PDB header:transferase Chain: A: PDB Molecule:gamma-glutamyl cyclotransferase; PDBTitle: gamma-glutamyl cyclotransferase 62 c1zaxZ_ not modelled 5.1 28 PDB header:structural protein Chain: Z: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form b

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