Secondary structure and disorder prediction

1

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10

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20

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30

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40

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50

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60

Sequence

M

K

T

S

D

N

E

R

I

K

Y

E

I

T

G

Q

A

V

L

Q

I

L

R

M

K

I

N

F

S

L

Q

T

L

I

K

Q

L

L

V

M

K

S

A

E

E

D

A

F

R

R

D

L

I

D

S

I

I

R

D

F

Secondary structure

SS confidence

Disorder

?

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?

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?

Disorder confidence

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70

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80

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90

Sequence

S

N

S

D

S

G

G

P

N

R

R

T

A

T

A

D

N

K

S

M

F

N

G

K

K

I

N

R

I

H

Secondary structure

SS confidence

Disorder

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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 2oxl chain A Region: 12 - 60 Aligned: 49 Modelled: 49 Confidence: 42.6% Identity: 20% PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance Phyre2 PDB 1z05 chain A domain 1 Region: 16 - 37 Aligned: 22 Modelled: 22 Confidence: 31.6% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: ROK associated domain Phyre2 PDB 3a7o chain B Region: 2 - 15 Aligned: 14 Modelled: 14 Confidence: 29.8% Identity: 29% PDB header:protein transport Chain: B: PDB Molecule:autophagy protein 16; PDBTitle: the crystal structure of the coiled-coil domain of2 saccharomyces cerevisiae atg16 Phyre2 PDB 1bia chain A domain 1 Region: 16 - 37 Aligned: 22 Modelled: 22 Confidence: 25.3% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Biotin repressor-like Phyre2 PDB 1z6r chain A domain 1 Region: 17 - 43 Aligned: 27 Modelled: 27 Confidence: 23.6% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: ROK associated domain Phyre2 PDB 2acv chain A domain 1 Region: 12 - 62 Aligned: 51 Modelled: 51 Confidence: 23.1% Identity: 6% Fold: UDP-Glycosyltransferase/glycogen phosphorylase Superfamily: UDP-Glycosyltransferase/glycogen phosphorylase Family: UDPGT-like Phyre2 PDB 2kzt chain B Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 23.1% Identity: 11% PDB header:apoptosis Chain: B: PDB Molecule:programmed cell death protein 4; PDBTitle: structure of the tandem ma-3 region of pdcd4 Phyre2 PDB 3hbj chain A Region: 5 - 61 Aligned: 57 Modelled: 57 Confidence: 20.5% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:flavonoid 3-o-glucosyltransferase; PDBTitle: structure of ugt78g1 complexed with udp Phyre2 PDB 2yud chain A Region: 14 - 38 Aligned: 25 Modelled: 25 Confidence: 20.0% Identity: 12% PDB header:rna binding protein Chain: A: PDB Molecule:yth domain-containing protein 1; PDBTitle: solution structure of the yth domain in yth domain-2 containing protein 1 (putative splicing factor yt521) Phyre2 PDB 1ub9 chain A Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 19.5% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MarR-like transcriptional regulators Phyre2 PDB 2iol chain B Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 18.4% Identity: 9% PDB header:antitumor protein Chain: B: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd4 (mouse); form2 1 Phyre2 PDB 2iol chain A Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 18.4% Identity: 9% PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd4 (mouse); form2 1 Phyre2 PDB 1xmk chain A domain 1 Region: 14 - 47 Aligned: 34 Modelled: 34 Confidence: 15.8% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Z-DNA binding domain Phyre2 PDB 2nsz chain A domain 1 Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 15.6% Identity: 11% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: MIF4G domain-like Phyre2 PDB 2nsz chain A Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 15.6% Identity: 11% PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: 1.15 angstrom crystal structure of the ma3 domain of pdcd4 Phyre2 PDB 2ion chain A Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 15.6% Identity: 11% PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd4 (mouse); form2 Phyre2 PDB 1usd chain A Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 14.5% Identity: 24% PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m Phyre2 PDB 2hm8 chain A Region: 14 - 60 Aligned: 47 Modelled: 47 Confidence: 14.2% Identity: 11% PDB header:apoptosis Chain: A: PDB Molecule:pdcd4 c-terminal ma-3 domain; PDBTitle: solution structure of the c-terminal ma-3 domain of pdcd4 Phyre2 PDB 3eit chain B Region: 23 - 57 Aligned: 35 Modelled: 35 Confidence: 14.0% Identity: 29% PDB header:unknown function Chain: B: PDB Molecule:putative atp/gtp binding protein; PDBTitle: the 2.6 angstrom crystal structure of chbp, the cif homologue from2 burkholderia pseudomallei Phyre2 PDB 3eyy chain A Region: 16 - 38 Aligned: 23 Modelled: 23 Confidence: 13.9% Identity: 13% PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition Phyre2 1 c2oxlA_ 2 d1z05a1 3 c3a7oB_ 4 d1biaa1 5 d1z6ra1 6 d2acva1 7 c2kztB_ 8 c3hbjA_ 9 c2yudA_ 10 d1ub9a_ 11 c2iolB_ 12 c2iolA_ 13 d1xmka1 14 d2nsza1 15 c2nszA_ 16 c2ionA_ 17 c1usdA_ 18 c2hm8A_ 19 c3eitB_ 20 c3eyyA_ 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

Detailed template information

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

1 c2oxlA_ 42.6 20 PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance 2 d1z05a1 31.6 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 3 c3a7oB_ 29.8 29 PDB header:protein transport Chain: B: PDB Molecule:autophagy protein 16; PDBTitle: the crystal structure of the coiled-coil domain of2 saccharomyces cerevisiae atg16 4 d1biaa1 25.3 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 5 d1z6ra1 23.6 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 6 d2acva1 23.1 6 Fold:UDP-Glycosyltransferase/glycogen phosphorylase Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase Family:UDPGT-like 7 c2kztB_ 23.1 11 PDB header:apoptosis Chain: B: PDB Molecule:programmed cell death protein 4; PDBTitle: structure of the tandem ma-3 region of pdcd4 8 c3hbjA_ 20.5 16 PDB header:transferase Chain: A: PDB Molecule:flavonoid 3-o-glucosyltransferase; PDBTitle: structure of ugt78g1 complexed with udp 9 c2yudA_ 20.0 12 PDB header:rna binding protein Chain: A: PDB Molecule:yth domain-containing protein 1; PDBTitle: solution structure of the yth domain in yth domain-2 containing protein 1 (putative splicing factor yt521) 10 d1ub9a_ 19.5 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 11 c2iolB_ 18.4 9 PDB header:antitumor protein Chain: B: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd4 (mouse); form2 1 12 c2iolA_ 18.4 9 PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd4 (mouse); form2 1 13 d1xmka1 15.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 14 d2nsza1 15.6 11 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:MIF4G domain-like 15 c2nszA_ 15.6 11 PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: 1.15 angstrom crystal structure of the ma3 domain of pdcd4 16 c2ionA_ 15.6 11 PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd4 (mouse); form2 17 c1usdA_ 14.5 24 PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m 18 c2hm8A_ 14.2 11 PDB header:apoptosis Chain: A: PDB Molecule:pdcd4 c-terminal ma-3 domain; PDBTitle: solution structure of the c-terminal ma-3 domain of pdcd4 19 c3eitB_ 14.0 29 PDB header:unknown function Chain: B: PDB Molecule:putative atp/gtp binding protein; PDBTitle: the 2.6 angstrom crystal structure of chbp, the cif homologue from2 burkholderia pseudomallei 20 c3eyyA_ 13.9 13 PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition 21 d2pq6a1 not modelled 13.4 10 Fold:UDP-Glycosyltransferase/glycogen phosphorylase Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase Family:UDPGT-like 22 d1i1ga1 not modelled 13.2 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 23 c3nj2B_ not modelled 13.1 26 PDB header:unknown function Chain: B: PDB Molecule:duf269-containing protein; PDBTitle: crystal structure of cce_0566 from the cyanobacterium cyanothece2 51142, a protein associated with nitrogen fixation from the duf2693 family 24 c3gqjA_ not modelled 11.8 31 PDB header:unknown function Chain: A: PDB Molecule:cell inhibiting factor (cif); PDBTitle: crystal structure of cell inhibiting factor (cif) from photorhabdus2 luminescens 25 c1qeyD_ not modelled 10.4 40 PDB header:gene regulation Chain: D: PDB Molecule:protein (regulatory protein mnt); PDBTitle: nmr structure determination of the tetramerization domain2 of the mnt repressor: an asymmetric a-helical assembly in3 slow exchange 26 c1qeyA_ not modelled 10.4 40 PDB header:gene regulation Chain: A: PDB Molecule:protein (regulatory protein mnt); PDBTitle: nmr structure determination of the tetramerization domain2 of the mnt repressor: an asymmetric a-helical assembly in3 slow exchange 27 c1qeyC_ not modelled 10.4 40 PDB header:gene regulation Chain: C: PDB Molecule:protein (regulatory protein mnt); PDBTitle: nmr structure determination of the tetramerization domain2 of the mnt repressor: an asymmetric a-helical assembly in3 slow exchange 28 c1qeyB_ not modelled 10.4 40 PDB header:gene regulation Chain: B: PDB Molecule:protein (regulatory protein mnt); PDBTitle: nmr structure determination of the tetramerization domain2 of the mnt repressor: an asymmetric a-helical assembly in3 slow exchange 29 d2cfxa1 not modelled 10.2 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 30 d1b79a_ not modelled 10.0 13 Fold:N-terminal domain of DnaB helicase Superfamily:N-terminal domain of DnaB helicase Family:N-terminal domain of DnaB helicase 31 c2veeC_ not modelled 9.6 18 PDB header:transport protein Chain: C: PDB Molecule:protoglobin; PDBTitle: structure of protoglobin from methanosarcina acetivorans2 c2a 32 c2l4aA_ not modelled 8.6 21 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 33 c4a1qB_ not modelled 8.6 38 PDB header:viral protein Chain: B: PDB Molecule:orf e73; PDBTitle: solution structure of e73 protein from sulfolobus spindle-2 shaped virus ragged hills, a hyperthermophilic3 crenarchaeal virus from yellowstone national park 34 d1q1va_ not modelled 8.3 12 Fold:Another 3-helical bundle Superfamily:DEK C-terminal domain Family:DEK C-terminal domain 35 c2ggfA_ not modelled 7.6 9 PDB header:translation Chain: A: PDB Molecule:programmed cell death 4, isoform 1; PDBTitle: solution structure of the ma3 domain of human programmed2 cell death 4 36 d2gxba1 not modelled 7.5 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 37 d1qo0d_ not modelled 7.4 13 Fold:Flavodoxin-like Superfamily:CheY-like Family:Positive regulator of the amidase operon AmiR 38 d2g7ga1 not modelled 7.3 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 39 c1zrwA_ not modelled 7.3 50 PDB header:antimicrobial protein, antibiotic Chain: A: PDB Molecule:spinigerin; PDBTitle: solution structure of spinigerin in h20/tfe 10% 40 c1zrvA_ not modelled 7.3 50 PDB header:antimicrobial protein, antibiotic Chain: A: PDB Molecule:spinigerin; PDBTitle: solution structure of spinigerin in h20/tfe 50% 41 c2ewnA_ not modelled 7.1 20 PDB header:ligase, transcription Chain: A: PDB Molecule:bira bifunctional protein; PDBTitle: ecoli biotin repressor with co-repressor analog 42 d2ev0a1 not modelled 6.9 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 43 d2iu5a1 not modelled 6.4 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 44 d2cg4a1 not modelled 6.4 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 45 d1ixsa_ not modelled 6.1 35 Fold:RuvA C-terminal domain-like Superfamily:DNA helicase RuvA subunit, C-terminal domain Family:DNA helicase RuvA subunit, C-terminal domain 46 c2l5yA_ not modelled 5.8 29 PDB header:signaling protein Chain: A: PDB Molecule:stromal interaction molecule 2; PDBTitle: nmr structure of calcium-loaded stim2 ef-sam. 47 d2cyya1 not modelled 5.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 48 d1zoqc1 not modelled 5.3 40 Fold:Nuclear receptor coactivator interlocking domain Superfamily:Nuclear receptor coactivator interlocking domain Family:Nuclear receptor coactivator interlocking 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