Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	S	K	E	Q	K	T	P	E	G	Q	A	P	E	E	I	I	M	D	Q	H	E	E	I	E	A	V	E	P	E	A	S	A	E	Q	V	D	P	R	D	E	K	V	A	N	L	E	A	Q	L	A	E	A	Q	T	R	E	R	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	I	L	R	V	K	A	E	M	E	N	L	R	R	R	T	E	L	D	I	E	K	A	H	K	F	A	L	E	K	F	I	N	E	L	L	P	V	I	D	S	L	D	R	A	L	E	V	A	D	K	A	N	P	D	M	S	A	M	V
Secondary structure
SS confidence
Disorder																																																	?		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		E	G	I	E	L	T	L	K	S	M	L	D	V	V	R	K	F	G	V	E	V	I	A	E	T	N	V	P	L	D	P	N	V	H	Q	A	I	A	M	V	E	S	D	D	V	A	P	G	N	V	L	G	I	M	Q	K	G	Y	T	L
Secondary structure
SS confidence
Disorder																								?	?	?	?	?														?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.
Sequence		N	G	R	T	I	R	A	A	M	V	T	V	A	K	A	K	A
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 1dkg chain B Region: 38 - 195 Aligned: 151 Modelled: 158 Confidence: 100.0% Identity: 99% PDB header:complex (hsp24/hsp70) Chain: B: PDB Molecule:nucleotide exchange factor grpe; PDBTitle: crystal structure of the nucleotide exchange factor grpe2 bound to the atpase domain of the molecular chaperone dnak Phyre2 PDB 3a6m chain B Region: 27 - 196 Aligned: 164 Modelled: 170 Confidence: 100.0% Identity: 27% PDB header:chaperone Chain: B: PDB Molecule:protein grpe; PDBTitle: crystal structure of grpe from thermus thermophilus hb8 Phyre2 PDB 1dkg chain A domain 1 Region: 139 - 197 Aligned: 59 Modelled: 59 Confidence: 99.8% Identity: 100% Fold: Head domain of nucleotide exchange factor GrpE Superfamily: Head domain of nucleotide exchange factor GrpE Family: Head domain of nucleotide exchange factor GrpE Phyre2 PDB 3hl6 chain B Region: 86 - 126 Aligned: 41 Modelled: 41 Confidence: 27.8% Identity: 22% PDB header:unknown function Chain: B: PDB Molecule:pathogenicity island protein; PDBTitle: staphylococcus aureus pathogenicity island 3 orf9 protein Phyre2 PDB 3swf chain A Region: 44 - 95 Aligned: 52 Modelled: 52 Confidence: 21.8% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:cgmp-gated cation channel alpha-1; PDBTitle: cnga1 621-690 containing clz domain Phyre2 PDB 1rso chain A Region: 59 - 95 Aligned: 37 Modelled: 37 Confidence: 19.6% Identity: 14% Fold: L27 domain Superfamily: L27 domain Family: L27 domain Phyre2 PDB 1nze chain A Region: 26 - 138 Aligned: 108 Modelled: 113 Confidence: 18.8% Identity: 18% Fold: Four-helical up-and-down bundle Superfamily: Oxygen-evolving enhancer protein 3, Family: Oxygen-evolving enhancer protein 3, Phyre2 PDB 1nze chain A Region: 26 - 138 Aligned: 108 Modelled: 113 Confidence: 18.8% Identity: 18% PDB header:oxidoreductase Chain: A: PDB Molecule:oxygen-evolving enhancer protein 3; PDBTitle: crystal structure of psbq polypeptide of photosystem ii2 from higher plants Phyre2 PDB 1x5t chain A domain 1 Region: 125 - 197 Aligned: 70 Modelled: 73 Confidence: 16.4% Identity: 19% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 2jvo chain A Region: 177 - 197 Aligned: 18 Modelled: 21 Confidence: 15.0% Identity: 22% PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: segmental isotope labeling of npl3 Phyre2 PDB 1w5f chain A Region: 147 - 185 Aligned: 39 Modelled: 39 Confidence: 14.9% Identity: 5% PDB header:cell division Chain: A: PDB Molecule:cell division protein ftsz; PDBTitle: ftsz, t7 mutated, domain swapped (t. maritima) Phyre2 PDB 2cpi chain A domain 1 Region: 177 - 188 Aligned: 12 Modelled: 12 Confidence: 14.4% Identity: 33% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 3e7l chain D Region: 95 - 141 Aligned: 47 Modelled: 47 Confidence: 14.2% Identity: 15% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 PDB 3mkx chain C Region: 35 - 77 Aligned: 43 Modelled: 43 Confidence: 14.1% Identity: 21% PDB header:antiviral protein Chain: C: PDB Molecule:bone marrow stromal antigen 2; PDBTitle: crystal structure of bst2/tetherin Phyre2 PDB 1fnx chain H domain 1 Region: 126 - 197 Aligned: 69 Modelled: 72 Confidence: 14.0% Identity: 14% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 2cbi chain A domain 1 Region: 35 - 122 Aligned: 83 Modelled: 88 Confidence: 13.5% Identity: 16% Fold: Hyaluronidase domain-like Superfamily: Hyaluronidase post-catalytic domain-like Family: Hyaluronidase post-catalytic domain-like Phyre2 PDB 1rk8 chain A Region: 126 - 186 Aligned: 61 Modelled: 61 Confidence: 13.4% Identity: 15% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 1wi8 chain A Region: 126 - 186 Aligned: 60 Modelled: 61 Confidence: 13.1% Identity: 17% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 1etx chain A Region: 97 - 139 Aligned: 43 Modelled: 43 Confidence: 12.6% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2cho chain A domain 1 Region: 35 - 109 Aligned: 72 Modelled: 75 Confidence: 12.6% Identity: 10% Fold: Hyaluronidase domain-like Superfamily: Hyaluronidase post-catalytic domain-like Family: Hyaluronidase post-catalytic domain-like Phyre2 1 c1dkgB_ 2 c3a6mB_ 3 d1dkga1 4 c3hl6B_ 5 c3swfA_ 6 d1rsoa_ 7 d1nzea_ 8 c1nzeA_ 9 d1x5ta1 10 c2jvoA_ 11 c1w5fA_ 12 d2cpia1 13 c3e7lD_ 14 c3mkxC_ 15 d1fnxh1 16 d2cbia1 17 d1rk8a_ 18 d1wi8a_ 19 d1etxa_ 20 d2choa1 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 63 64 65

Detailed template information

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

1 c1dkgB_ 100.0 99 PDB header:complex (hsp24/hsp70) Chain: B: PDB Molecule:nucleotide exchange factor grpe; PDBTitle: crystal structure of the nucleotide exchange factor grpe2 bound to the atpase domain of the molecular chaperone dnak 2 c3a6mB_ 100.0 27 PDB header:chaperone Chain: B: PDB Molecule:protein grpe; PDBTitle: crystal structure of grpe from thermus thermophilus hb8 3 d1dkga1 99.8 100 Fold:Head domain of nucleotide exchange factor GrpE Superfamily:Head domain of nucleotide exchange factor GrpE Family:Head domain of nucleotide exchange factor GrpE 4 c3hl6B_ 27.8 22 PDB header:unknown function Chain: B: PDB Molecule:pathogenicity island protein; PDBTitle: staphylococcus aureus pathogenicity island 3 orf9 protein 5 c3swfA_ 21.8 15 PDB header:transport protein Chain: A: PDB Molecule:cgmp-gated cation channel alpha-1; PDBTitle: cnga1 621-690 containing clz domain 6 d1rsoa_ 19.6 14 Fold:L27 domain Superfamily:L27 domain Family:L27 domain 7 d1nzea_ 18.8 18 Fold:Four-helical up-and-down bundle Superfamily:Oxygen-evolving enhancer protein 3, Family:Oxygen-evolving enhancer protein 3, 8 c1nzeA_ 18.8 18 PDB header:oxidoreductase Chain: A: PDB Molecule:oxygen-evolving enhancer protein 3; PDBTitle: crystal structure of psbq polypeptide of photosystem ii2 from higher plants 9 d1x5ta1 16.4 19 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 10 c2jvoA_ 15.0 22 PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: segmental isotope labeling of npl3 11 c1w5fA_ 14.9 5 PDB header:cell division Chain: A: PDB Molecule:cell division protein ftsz; PDBTitle: ftsz, t7 mutated, domain swapped (t. maritima) 12 d2cpia1 14.4 33 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 13 c3e7lD_ 14.2 15 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 14 c3mkxC_ 14.1 21 PDB header:antiviral protein Chain: C: PDB Molecule:bone marrow stromal antigen 2; PDBTitle: crystal structure of bst2/tetherin 15 d1fnxh1 14.0 14 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 16 d2cbia1 13.5 16 Fold:Hyaluronidase domain-like Superfamily:Hyaluronidase post-catalytic domain-like Family:Hyaluronidase post-catalytic domain-like 17 d1rk8a_ 13.4 15 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 18 d1wi8a_ 13.1 17 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 19 d1etxa_ 12.6 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 20 d2choa1 12.6 10 Fold:Hyaluronidase domain-like Superfamily:Hyaluronidase post-catalytic domain-like Family:Hyaluronidase post-catalytic domain-like 21 d2qeec1 not modelled 11.6 19 Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:Uronate isomerase-like 22 d1w5fa2 not modelled 11.3 5 Fold:Bacillus chorismate mutase-like Superfamily:Tubulin C-terminal domain-like Family:Tubulin, C-terminal domain 23 d1ntca_ not modelled 11.0 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 24 d1ttea1 not modelled 10.7 22 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 25 c3bs9A_ not modelled 10.6 17 PDB header:rna binding protein Chain: A: PDB Molecule:nucleolysin tia-1 isoform p40; PDBTitle: x-ray structure of human tia-1 rrm2 26 d2j01s1 not modelled 9.8 30 Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:Ribosomal protein L18 and S11 27 c3lraA_ not modelled 9.5 16 PDB header:membrane protein Chain: A: PDB Molecule:disks large homolog 1, maguk p55 subfamily member 7, PDBTitle: structural basis for assembling a human tripartite complex dlg1-mpp7-2 mals3 28 d2cqca1 not modelled 9.5 21 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 29 d1we1a_ not modelled 9.1 6 Fold:Heme oxygenase-like Superfamily:Heme oxygenase-like Family:Eukaryotic type heme oxygenase 30 c3he5A_ not modelled 9.0 24 PDB header:de novo protein Chain: A: PDB Molecule:synzip1; PDBTitle: heterospecific coiled-coil pair synzip2:synzip1 31 c2x7aB_ not modelled 8.8 21 PDB header:immune system Chain: B: PDB Molecule:bone marrow stromal antigen 2; PDBTitle: structural basis of hiv-1 tethering to membranes by the2 bst2-tetherin ectodomain 32 d1fxla1 not modelled 8.6 13 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 33 d1pzqa_ not modelled 8.6 25 Fold:Dimerisation interlock Superfamily:Docking domain A of the erythromycin polyketide synthase (DEBS) Family:Docking domain A of the erythromycin polyketide synthase (DEBS) 34 c1zvuA_ not modelled 8.5 23 PDB header:isomerase Chain: A: PDB Molecule:topoisomerase iv subunit a; PDBTitle: structure of the full-length e. coli parc subunit 35 c3movB_ not modelled 7.8 17 PDB header:structural protein Chain: B: PDB Molecule:lamin-b1; PDBTitle: crystal structure of human lamin-b1 coil 2 segment 36 c2jl8S_ not modelled 7.8 30 PDB header:ribosome Chain: S: PDB Molecule:50s ribosomal protein l18; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome (part 4 of 4).3 this file contains the 50s subunit. 37 d2d6fa1 not modelled 7.6 10 Fold:Sm-like fold Superfamily:GatD N-terminal domain-like Family:GatD N-terminal domain-like 38 c3q9vB_ not modelled 7.5 29 PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding response regulator; PDBTitle: crystal structure of rra c-terminal domain(123-221) from deinococcus2 radiodurans 39 c3m9bK_ not modelled 7.4 11 PDB header:chaperone Chain: K: PDB Molecule:proteasome-associated atpase; PDBTitle: crystal structure of the amino terminal coiled coil domain and the2 inter domain of the mycobacterium tuberculosis proteasomal atpase mpa 40 d1h2vz_ not modelled 7.3 15 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 41 c3md1B_ not modelled 7.1 13 PDB header:rna binding protein Chain: B: PDB Molecule:nuclear and cytoplasmic polyadenylated rna-binding protein PDBTitle: crystal structure of the second rrm domain of yeast poly(u)-binding2 protein (pub1) 42 d1igub_ not modelled 7.0 10 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:Transcriptional repressor protein KorB 43 d1fipa_ not modelled 6.9 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 44 d1tafa_ not modelled 6.7 7 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 45 d2zjrl1 not modelled 6.6 30 Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:Ribosomal protein L18 and S11 46 d1cvja1 not modelled 6.5 11 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 47 d2otaa1 not modelled 6.5 33 Fold:YejL-like Superfamily:YejL-like Family:YejL-like 48 c3swyB_ not modelled 6.3 12 PDB header:transport protein Chain: B: PDB Molecule:cyclic nucleotide-gated cation channel alpha-3; PDBTitle: cnga3 626-672 containing clz domain 49 d1ovya_ not modelled 6.2 40 Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:Ribosomal protein L18 and S11 50 c2kxyA_ not modelled 6.1 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of sur18c from streptococcus thermophilus.2 northeast structural genomics consortium target sur18c 51 d2cqba1 not modelled 6.0 22 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 52 c1qzuB_ not modelled 5.9 25 PDB header:lyase Chain: B: PDB Molecule:hypothetical protein mds018; PDBTitle: crystal structure of human phosphopantothenoylcysteine decarboxylase 53 d1igqa_ not modelled 5.9 17 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:Transcriptional repressor protein KorB 54 d1ov2a_ not modelled 5.9 13 Fold:RAP domain-like Superfamily:RAP domain-like Family:RAP domain 55 c1xe1A_ not modelled 5.8 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pf0907; PDBTitle: hypothetical protein from pyrococcus furiosus pfu-880080-001 56 d1xe1a_ not modelled 5.8 31 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 57 d1bv8a_ not modelled 5.8 11 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Alpha-macroglobulin receptor domain Family:Alpha-macroglobulin receptor domain 58 d2j0sd1 not modelled 5.6 15 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 59 c1m7lA_ not modelled 5.5 11 PDB header:sugar binding protein Chain: A: PDB Molecule:pulmonary surfactant-associated protein d; PDBTitle: solution structure of the coiled-coil trimerization domain2 from lung surfactant protein d 60 d1kyza2 not modelled 5.4 13 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Plant O-methyltransferase, C-terminal domain 61 d1jeyb1 not modelled 5.3 8 Fold:SPOC domain-like Superfamily:SPOC domain-like Family:Ku80 subunit middle domain 62 d1huwa_ not modelled 5.2 12 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Long-chain cytokines 63 c3cxjB_ not modelled 5.2 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 methanothermobacter thermautotrophicus 64 c3nmdA_ not modelled 5.2 17 PDB header:transferase Chain: A: PDB Molecule:cgmp dependent protein kinase; PDBTitle: crystal structure of the leucine zipper domain of cgmp dependent2 protein kinase i beta 65 d1jeya1 not modelled 5.2 17 Fold:SPOC domain-like Superfamily:SPOC domain-like Family:Ku70 subunit middle 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