Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A9W0
DateThu Jan 5 11:11:32 GMT 2012
Unique Job ID6fc83cfacf49f60b

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1m0sa1
Top template information
Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
Confidence and coverage
Confidence:100.0% Coverage: 53%
133 residues ( 53% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
230 residues ( 92%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MTEAQRHQILLEMLAQLGFVTVEKVVERLGISPATARRDINKLDESGKLKKVRNGAEAIT
Secondary structure 
SS confidence 
Disorder  ??
?
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  QQRPRWTPMNLHQAQNHDEKVRIAKAASQLVNPGESVVINCGSTAFLLGREMCGKPVQII
Secondary structure 
SS confidence 
Disorder  ????????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  TNYLPLANYLIDQEHDSVIIMGGQYNKSQSITLSPQGSENSLYAGHWMFTSGKGLTAEGL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  YKTDMLTAMAEQKMLSVVGKLVVLVDSSKIGERAGMLFSRADQIDMLITGKNANPEILQQ
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.
Sequence  LEAQGVSILRV
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

RankAligned region

PDB 1m0s chain A domain 1

3D model

Region: 76 - 232
Aligned: 133
Modelled: 137
Confidence: 100.0%
Identity: 20%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain

Phyre2

PDB 1lk5 chain A domain 1

3D model

Region: 76 - 234
Aligned: 138
Modelled: 145
Confidence: 99.9%
Identity: 21%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain

Phyre2

PDB 1uj4 chain A domain 1

3D model

Region: 74 - 216
Aligned: 128
Modelled: 128
Confidence: 99.9%
Identity: 16%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain

Phyre2

PDB 3hhe chain A

3D model

Region: 78 - 213
Aligned: 116
Modelled: 116
Confidence: 99.8%
Identity: 15%
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from bartonella2 henselae

Phyre2

PDB 2f8m chain B

3D model

Region: 78 - 221
Aligned: 124
Modelled: 124
Confidence: 99.8%
Identity: 17%
PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: ribose 5-phosphate isomerase from plasmodium falciparum

Phyre2

PDB 1lk5 chain C

3D model

Region: 78 - 213
Aligned: 116
Modelled: 116
Confidence: 99.8%
Identity: 17%
PDB header:isomerase
Chain: C: PDB Molecule:d-ribose-5-phosphate isomerase;
PDBTitle: structure of the d-ribose-5-phosphate isomerase from2 pyrococcus horikoshii

Phyre2

PDB 1m0s chain A

3D model

Region: 76 - 213
Aligned: 119
Modelled: 119
Confidence: 99.8%
Identity: 20%
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: northeast structural genomics consortium (nesg id ir21)

Phyre2

PDB 3kwm chain C

3D model

Region: 76 - 213
Aligned: 119
Modelled: 119
Confidence: 99.8%
Identity: 14%
PDB header:isomerase
Chain: C: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-isomerase a

Phyre2

PDB 1lkz chain B

3D model

Region: 76 - 213
Aligned: 119
Modelled: 119
Confidence: 99.8%
Identity: 19%
PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase a;
PDBTitle: crystal structure of d-ribose-5-phosphate isomerase (rpia)2 from escherichia coli.

Phyre2

PDB 3l7o chain B

3D model

Region: 78 - 210
Aligned: 113
Modelled: 113
Confidence: 99.8%
Identity: 19%
PDB header:isomerase
Chain: B: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from streptococcus2 mutans ua159

Phyre2

PDB 2pjm chain A

3D model

Region: 75 - 213
Aligned: 124
Modelled: 124
Confidence: 99.8%
Identity: 24%
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: structure of ribose 5-phosphate isomerase a from2 methanocaldococcus jannaschii

Phyre2

PDB 1uj6 chain A

3D model

Region: 78 - 210
Aligned: 119
Modelled: 119
Confidence: 99.8%
Identity: 20%
PDB header:isomerase
Chain: A: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: crystal structure of thermus thermophilus ribose-5-phosphate isomerase2 complexed with arabinose-5-phosphate

Phyre2

PDB 1stz chain A domain 1

3D model

Region: 5 - 78
Aligned: 74
Modelled: 74
Confidence: 99.2%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Heat-inducible transcription repressor HrcA, N-terminal domain

Phyre2

PDB 1j5y chain A domain 1

3D model

Region: 1 - 58
Aligned: 58
Modelled: 58
Confidence: 99.1%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2

PDB 1bia chain A domain 1

3D model

Region: 1 - 62
Aligned: 62
Modelled: 62
Confidence: 99.1%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2

PDB 1j5y chain A

3D model

Region: 3 - 84
Aligned: 82
Modelled: 82
Confidence: 99.0%
Identity: 15%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution

Phyre2

PDB 3u7j chain A

3D model

Region: 76 - 210
Aligned: 115
Modelled: 115
Confidence: 99.0%
Identity: 20%
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from burkholderia2 thailandensis

Phyre2

PDB 1xtz chain A

3D model

Region: 78 - 210
Aligned: 114
Modelled: 114
Confidence: 98.9%
Identity: 19%
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase;
PDBTitle: crystal structure of the s. cerevisiae d-ribose-5-phosphate isomerase:2 comparison with the archeal and bacterial enzymes

Phyre2

PDB 1o8b chain B domain 1

3D model

Region: 76 - 210
Aligned: 111
Modelled: 115
Confidence: 98.5%
Identity: 20%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain

Phyre2

PDB 2d1h chain A domain 1

3D model

Region: 2 - 84
Aligned: 82
Modelled: 0
Confidence: 98.2%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: TrmB-like

Phyre2
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d1m0sa1
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d1lk5a1
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d1uj4a1
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c3hheA_
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c2f8mB_
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c1lk5C_
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c1m0sA_
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c3kwmC_
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c1lkzB_
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c3l7oB_
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c2pjmA_
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c1uj6A_
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d1stza1
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d1j5ya1
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d1biaa1
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c1j5yA_
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c3u7jA_
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c1xtzA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1m0sa1
100.0 20 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
2d1lk5a1
99.9 21 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
3d1uj4a1
99.9 16 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
4c3hheA_
99.8 15 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from bartonella2 henselae
5c2f8mB_
99.8 17 PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: ribose 5-phosphate isomerase from plasmodium falciparum
6c1lk5C_
99.8 17 PDB header:isomerase
Chain: C: PDB Molecule:d-ribose-5-phosphate isomerase;
PDBTitle: structure of the d-ribose-5-phosphate isomerase from2 pyrococcus horikoshii
7c1m0sA_
99.8 20 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: northeast structural genomics consortium (nesg id ir21)
8c3kwmC_
99.8 14 PDB header:isomerase
Chain: C: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-isomerase a
9c1lkzB_
99.8 19 PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase a;
PDBTitle: crystal structure of d-ribose-5-phosphate isomerase (rpia)2 from escherichia coli.
10c3l7oB_
99.8 19 PDB header:isomerase
Chain: B: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from streptococcus2 mutans ua159
11c2pjmA_
99.8 24 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: structure of ribose 5-phosphate isomerase a from2 methanocaldococcus jannaschii
12c1uj6A_
99.8 20 PDB header:isomerase
Chain: A: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: crystal structure of thermus thermophilus ribose-5-phosphate isomerase2 complexed with arabinose-5-phosphate
13d1stza1
99.2 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
14d1j5ya1
99.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
15d1biaa1
99.1 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
16c1j5yA_
99.0 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
17c3u7jA_
99.0 20 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from burkholderia2 thailandensis
18c1xtzA_
98.9 19 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase;
PDBTitle: crystal structure of the s. cerevisiae d-ribose-5-phosphate isomerase:2 comparison with the archeal and bacterial enzymes
19d1o8bb1
98.5 20 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
20d2d1ha1
98.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
21c3f8mA_
not modelled 98.1 11 PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis
22c2h09A_
not modelled 98.1 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
23d1vb5a_
not modelled 98.1 17 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
24c2vbzA_
not modelled 98.0 23 PDB header:dna-binding protein
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan
25d2cg4a1
not modelled 98.0 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
26c2x4hA_
not modelled 98.0 18 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
27c2l4aA_
not modelled 98.0 18 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
28c1f5tA_
not modelled 98.0 14 PDB header:transcription/dna
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
29c3bwgA_
not modelled 98.0 17 PDB header:transcription regulator
Chain: A: PDB Molecule:uncharacterized hth-type transcriptional regulator yydk;
PDBTitle: the crystal structure of possible transcriptional regulator yydk from2 bacillus subtilis subsp. subtilis str. 168
30d2cfxa1
not modelled 97.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
31c2du9A_
not modelled 97.9 20 PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
32d1t5oa_
not modelled 97.9 16 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
33d1t9ka_
not modelled 97.9 16 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
34c3edpB_
not modelled 97.9 13 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:lin2111 protein;
PDBTitle: the crystal structure of the protein lin2111 (functionally unknown)2 from listeria innocua clip11262
35d2hs5a1
not modelled 97.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
36c3neuA_
not modelled 97.9 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
37d1i1ga1
not modelled 97.9 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
38c3ecsD_
not modelled 97.9 12 PDB header:translation
Chain: D: PDB Molecule:translation initiation factor eif-2b subunit
PDBTitle: crystal structure of human eif2b alpha
39c3by6C_
not modelled 97.9 14 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
40c2it0A_
not modelled 97.8 14 PDB header:transcription/dna
Chain: A: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
41d2cyya1
not modelled 97.8 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
42c2hs5A_
not modelled 97.8 12 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcriptional regulator gntr;
PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator gntr from rhodococcus sp. rha1
43c3c7jA_
not modelled 97.8 10 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of transcriptional regulator (gntr family member)2 from pseudomonas syringae pv. tomato str. dc3000
44d1jhfa1
not modelled 97.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
45c2wteB_
not modelled 97.8 21 PDB header:antiviral protein
Chain: B: PDB Molecule:csa3;
PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
46c3eetA_
not modelled 97.8 13 PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
47c2e1cA_
not modelled 97.8 26 PDB header:transcription/dna
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519;
PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
48c3lmmA_
not modelled 97.7 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35
49c2e7xA_
not modelled 97.7 13 PDB header:transcription regulator
Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator;
PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand
50c3a11D_
not modelled 97.7 11 PDB header:isomerase
Chain: D: PDB Molecule:translation initiation factor eif-2b, delta
PDBTitle: crystal structure of ribose-1,5-bisphosphate isomerase from2 thermococcus kodakaraensis kod1
51c2cg4B_
not modelled 97.7 22 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
52d1hw1a1
not modelled 97.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
53c2w48D_
not modelled 97.7 20 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
54c3cuoB_
not modelled 97.6 13 PDB header:transcription regulator
Chain: B: PDB Molecule:uncharacterized hth-type transcriptional regulator ygav;
PDBTitle: crystal structure of the predicted dna-binding transcriptional2 regulator from e. coli
55c2ia0A_
not modelled 97.6 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864;
PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864)
56c2yvkA_
not modelled 97.6 18 PDB header:isomerase
Chain: A: PDB Molecule:methylthioribose-1-phosphate isomerase;
PDBTitle: crystal structure of 5-methylthioribose 1-phosphate2 isomerase product complex from bacillus subtilis
57c2cfxD_
not modelled 97.6 18 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
58c1stzB_
not modelled 97.6 26 PDB header:transcription
Chain: B: PDB Molecule:heat-inducible transcription repressor hrca homolog;
PDBTitle: crystal structure of a hypothetical protein at 2.2 a resolution
59c3i4pA_
not modelled 97.6 22 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
60c3eqxB_
not modelled 97.6 19 PDB header:dna binding protein
Chain: B: PDB Molecule:fic domain containing transcriptional regulator;
PDBTitle: crystal structure of a fic family protein (so_4266) from shewanella2 oneidensis at 1.6 a resolution
61c2dbbA_
not modelled 97.6 22 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
62c2p6tH_
not modelled 97.6 22 PDB header:transcription
Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family;
PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis
63d1z05a1
not modelled 97.6 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
64d1v4ra1
not modelled 97.5 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
65d1ub9a_
not modelled 97.5 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
66c2oqgA_
not modelled 97.5 19 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
67c1e2xA_
not modelled 97.5 17 PDB header:transcriptional regulation
Chain: A: PDB Molecule:fatty acid metabolism regulator protein;
PDBTitle: fadr, fatty acid responsive transcription factor from e.2 coli
68d2ev0a1
not modelled 97.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
69c1i1gA_
not modelled 97.5 26 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
70d1r1ua_
not modelled 97.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
71d3bwga1
not modelled 97.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
72c3cdkD_
not modelled 97.4 17 PDB header:transferase
Chain: D: PDB Molecule:succinyl-coa:3-ketoacid-coenzyme a transferase
PDBTitle: crystal structure of the co-expressed succinyl-coa2 transferase a and b complex from bacillus subtilis
73d1ulya_
not modelled 97.4 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein PH1932
74c2gqqB_
not modelled 97.4 20 PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
75d2p4wa1
not modelled 97.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
76c2di3A_
not modelled 97.4 13 PDB header:transcription
Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family;
PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
77c3fmsA_
not modelled 97.4 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
78c3f6vA_
not modelled 97.4 19 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
79c1g3wA_
not modelled 97.4 18 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
80c3hruA_
not modelled 97.4 20 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
81c3ihuA_
not modelled 97.3 12 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of dna binding protein (yp_298823.1) from ralstonia2 eutropha jmp134 at 1.92 a resolution
82d1sfxa_
not modelled 97.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
83d1mkma1
not modelled 97.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
84c1r22B_
not modelled 97.3 18 PDB header:transcription repressor
Chain: B: PDB Molecule:transcriptional repressor smtb;
PDBTitle: crystal structure of the cyanobacterial metallothionein2 repressor smtb (c14s/c61s/c121s mutant) in the zn2alpha5-3 form
85c1fx7C_
not modelled 97.3 14 PDB header:signaling protein
Chain: C: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of the iron-dependent regulator (ider)2 from mycobacterium tuberculosis
86c3f6oB_
not modelled 97.2 19 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
87d1r1ta_
not modelled 97.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
88d1g3wa1
not modelled 97.2 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
89c3eyyA_
not modelled 97.1 24 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
90d2htja1
not modelled 97.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:FaeA-like
91c2qwwB_
not modelled 97.1 18 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution
92c2ev5B_
not modelled 97.1 20 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
93d2p5ka1
not modelled 97.1 31 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
94d1lnwa_
not modelled 97.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
95c2nyxB_
not modelled 97.1 17 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
96d1okra_
not modelled 97.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
97c2kkoB_
not modelled 97.1 25 PDB header:dna binding protein
Chain: B: PDB Molecule:possible transcriptional regulatory protein
PDBTitle: solution nmr structure of the homodimeric winged helix-turn-2 helix dna-binding domain (fragment 1-100) mb0332 from3 mycobacterium bovis, a possible arsr-family transcriptional4 regulator. northeast structural genomics consortium target5 mbr242e.
98c3bj6B_
not modelled 97.1 17 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
99d2isya1
not modelled 97.1 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
100c2w57A_
not modelled 97.0 25 PDB header:metal transport
Chain: A: PDB Molecule:ferric uptake regulation protein;
PDBTitle: crystal structure of the vibrio cholerae ferric uptake2 regulator (fur) reveals structural rearrangement of the3 dna-binding domains
101c2zkzC_
not modelled 97.0 15 PDB header:transcription
Chain: C: PDB Molecule:transcriptional repressor pagr;
PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
102d2fxaa1
not modelled 97.0 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
103c3bddD_
not modelled 97.0 27 PDB header:transcription
Chain: D: PDB Molecule:regulatory protein marr;
PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution
104d1k6da_
not modelled 97.0 20 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase alpha subunit-like
105c2dt5A_
not modelled 97.0 13 PDB header:dna binding protein
Chain: A: PDB Molecule:at-rich dna-binding protein;
PDBTitle: crystal structure of ttha1657 (at-rich dna-binding protein) from2 thermus thermophilus hb8
106c2fa5B_
not modelled 96.9 17 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator marr/emrr family;
PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris
107c3oopA_
not modelled 96.9 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2960 protein;
PDBTitle: the structure of a protein with unknown function from listeria innocua2 clip11262
108c3jthA_
not modelled 96.9 15 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
109c3g3zA_
not modelled 96.9 19 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
110c1mkmA_
not modelled 96.9 13 PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr
111c3s2wB_
not modelled 96.9 26 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the crystal structure of a marr transcriptional regulator from2 methanosarcina mazei go1
112d2etha1
not modelled 96.9 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
113d1s3ja_
not modelled 96.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
114c2rdpA_
not modelled 96.8 17 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
115c3r0aB_
not modelled 96.8 17 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
116d1ooya1
not modelled 96.8 13 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase beta subunit-like
117c2fxaB_
not modelled 96.8 22 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
118c2fe3B_
not modelled 96.8 24 PDB header:dna binding protein
Chain: B: PDB Molecule:peroxide operon regulator;
PDBTitle: the crystal structure of bacillus subtilis perr-zn reveals a novel2 zn(cys)4 structural redox switch
119c1o57A_
not modelled 96.8 18 PDB header:dna binding protein
Chain: A: PDB Molecule:pur operon repressor;
PDBTitle: crystal structure of the purine operon repressor of2 bacillus subtilis
120d1ku9a_
not modelled 96.8 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223

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


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
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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