Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP39361
DateThu Jan 5 11:59:52 GMT 2012
Unique Job ID1a4433c0867070c8

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: 52%
135 residues ( 52% 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.
235 residues ( 90%) 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  MSQQRPDRIKQMLHYLWQHRHLSTQQAMELFGYAEATVRRDFQYIVNQYPGMIRGHGCLD
Secondary structure 
SS confidence 
Disorder  ????
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  FDDSTDDKEYVFDVKRTLQSVAKREIAALARTMIKDGDCFFLDSGSTCLELAKCLADARV
Secondary structure 
SS confidence 
Disorder 
????????
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  KVICNDIKIANELGCFPHVESYIIGGLIRPGYFSVGESLALEMINAFSVERAFISCDALS
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LETGITNATMFEVGVKTRIIQRSREVILMADHSKFDAVEPHAVATLSCIKTIISDSGLPE
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260
Sequence  TIAQRYQRAGCQLFLPHSIK
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: 79 - 237
Aligned: 135
Modelled: 139
Confidence: 100.0%
Identity: 15%
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: 79 - 239
Aligned: 140
Modelled: 147
Confidence: 100.0%
Identity: 17%
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: 77 - 221
Aligned: 130
Modelled: 130
Confidence: 99.9%
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 3hhe chain A

3D model

Region: 80 - 218
Aligned: 119
Modelled: 119
Confidence: 99.9%
Identity: 18%
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: 81 - 226
Aligned: 126
Modelled: 126
Confidence: 99.8%
Identity: 13%
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: 81 - 218
Aligned: 118
Modelled: 118
Confidence: 99.8%
Identity: 16%
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 3kwm chain C

3D model

Region: 79 - 215
Aligned: 117
Modelled: 117
Confidence: 99.8%
Identity: 16%
PDB header:isomerase
Chain: C: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-isomerase a

Phyre2

PDB 1m0s chain A

3D model

Region: 79 - 215
Aligned: 117
Modelled: 117
Confidence: 99.8%
Identity: 15%
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: northeast structural genomics consortium (nesg id ir21)

Phyre2

PDB 3l7o chain B

3D model

Region: 81 - 215
Aligned: 115
Modelled: 115
Confidence: 99.8%
Identity: 14%
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 1lkz chain B

3D model

Region: 79 - 218
Aligned: 120
Modelled: 120
Confidence: 99.8%
Identity: 15%
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 2pjm chain A

3D model

Region: 78 - 218
Aligned: 126
Modelled: 126
Confidence: 99.8%
Identity: 17%
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: 81 - 215
Aligned: 121
Modelled: 121
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 3u7j chain A

3D model

Region: 79 - 215
Aligned: 117
Modelled: 117
Confidence: 99.0%
Identity: 16%
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 1j5y chain A domain 1

3D model

Region: 5 - 63
Aligned: 59
Modelled: 59
Confidence: 99.0%
Identity: 15%
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: 5 - 100
Aligned: 91
Modelled: 96
Confidence: 99.0%
Identity: 13%
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 1stz chain A domain 1

3D model

Region: 7 - 63
Aligned: 57
Modelled: 57
Confidence: 98.9%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Heat-inducible transcription repressor HrcA, N-terminal domain

Phyre2

PDB 1bia chain A domain 1

3D model

Region: 1 - 64
Aligned: 62
Modelled: 64
Confidence: 98.9%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2

PDB 1xtz chain A

3D model

Region: 81 - 215
Aligned: 115
Modelled: 116
Confidence: 98.8%
Identity: 20%
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 2w48 chain D

3D model

Region: 6 - 251
Aligned: 207
Modelled: 218
Confidence: 98.6%
Identity: 17%
PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae

Phyre2

PDB 1o8b chain B domain 1

3D model

Region: 79 - 215
Aligned: 112
Modelled: 118
Confidence: 98.5%
Identity: 15%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain

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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c3kwmC_
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c1m0sA_
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c3l7oB_
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c1lkzB_
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c2pjmA_
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c1uj6A_
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c3u7jA_
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d1j5ya1
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c1j5yA_
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d1stza1
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d1biaa1
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c1xtzA_
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c2w48D_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1m0sa1
100.0 15 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
2d1lk5a1
100.0 17 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
3d1uj4a1
99.9 20 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
4c3hheA_
99.9 18 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 13 PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: ribose 5-phosphate isomerase from plasmodium falciparum
6c1lk5C_
99.8 16 PDB header:isomerase
Chain: C: PDB Molecule:d-ribose-5-phosphate isomerase;
PDBTitle: structure of the d-ribose-5-phosphate isomerase from2 pyrococcus horikoshii
7c3kwmC_
99.8 16 PDB header:isomerase
Chain: C: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-isomerase a
8c1m0sA_
99.8 15 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: northeast structural genomics consortium (nesg id ir21)
9c3l7oB_
99.8 14 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
10c1lkzB_
99.8 15 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.
11c2pjmA_
99.8 17 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
13c3u7jA_
99.0 16 PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from burkholderia2 thailandensis
14d1j5ya1
99.0 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
15c1j5yA_
99.0 13 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
16d1stza1
98.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
17d1biaa1
98.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
18c1xtzA_
98.8 20 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
19c2w48D_
98.6 17 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
20d1o8bb1
98.5 15 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain
21d1vb5a_
not modelled 98.1 22 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
22d1t5oa_
not modelled 98.0 17 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
23d1t9ka_
not modelled 98.0 14 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
24c1f5tA_
not modelled 97.9 6 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
25c2yvkA_
not modelled 97.9 19 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
26c3cdkD_
not modelled 97.9 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
27c2h09A_
not modelled 97.9 7 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
28c3a11D_
not modelled 97.8 16 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
29d2d1ha1
not modelled 97.8 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
30c3f8mA_
not modelled 97.8 17 PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis
31c2it0A_
not modelled 97.7 8 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
32c3neuA_
not modelled 97.7 13 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
33c2vbzA_
not modelled 97.7 7 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
34c2du9A_
not modelled 97.7 10 PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
35d2hs5a1
not modelled 97.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
36c3edpB_
not modelled 97.7 10 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
37c3bwgA_
not modelled 97.6 12 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
38c3ecsD_
not modelled 97.6 22 PDB header:translation
Chain: D: PDB Molecule:translation initiation factor eif-2b subunit
PDBTitle: crystal structure of human eif2b alpha
39d2cg4a1
not modelled 97.6 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
40c2e1cA_
not modelled 97.5 11 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
41c2l4aA_
not modelled 97.5 11 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
42c2hs5A_
not modelled 97.5 16 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
43c2x4hA_
not modelled 97.5 9 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
44c3ereD_
not modelled 97.5 15 PDB header:dna binding protein/dna
Chain: D: PDB Molecule:arginine repressor;
PDBTitle: crystal structure of the arginine repressor protein from mycobacterium2 tuberculosis in complex with the dna operator
45c3eetA_
not modelled 97.5 12 PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
46d2cfxa1
not modelled 97.4 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
47c3by6C_
not modelled 97.4 13 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
48d1i1ga1
not modelled 97.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
49d2cyya1
not modelled 97.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
50c3c7jA_
not modelled 97.4 16 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
51c2cg4B_
not modelled 97.4 12 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
52d2p5ka1
not modelled 97.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
53d1ooya1
not modelled 97.4 19 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase beta subunit-like
54d1hw1a1
not modelled 97.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
55c2cfxD_
not modelled 97.3 11 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
56c2dbbA_
not modelled 97.3 10 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
57c1fx7C_
not modelled 97.3 8 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
58c3cuoB_
not modelled 97.3 8 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
59c1stzB_
not modelled 97.3 19 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
60c2wteB_
not modelled 97.3 8 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.
61c1i1gA_
not modelled 97.2 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
62c2e7xA_
not modelled 97.2 10 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
63c1b4aA_
not modelled 97.2 13 PDB header:repressor
Chain: A: PDB Molecule:arginine repressor;
PDBTitle: structure of the arginine repressor from bacillus stearothermophilus
64d1b4aa1
not modelled 97.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
65c2ia0A_
not modelled 97.2 14 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)
66c2p6tH_
not modelled 97.2 13 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
67d1k6da_
not modelled 97.2 15 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase alpha subunit-like
68c1e2xA_
not modelled 97.2 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
69c3lmmA_
not modelled 97.2 12 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
70c2oqgA_
not modelled 97.2 8 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
71c3eqxB_
not modelled 97.2 8 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
72d1z05a1
not modelled 97.2 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
73c2di3A_
not modelled 97.2 9 PDB header:transcription
Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family;
PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
74c3i4pA_
not modelled 97.1 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
75d2gnpa1
not modelled 97.1 14 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:SorC sugar-binding domain-like
76c1g3wA_
not modelled 97.1 7 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
77c3fmsA_
not modelled 97.1 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
78d1v4ra1
not modelled 97.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
79d1g3wa1
not modelled 97.1 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
80c2gqqB_
not modelled 97.1 12 PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
81d3bwga1
not modelled 97.0 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
82d2isya1
not modelled 97.0 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
83c3hruA_
not modelled 97.0 11 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
84c3ihuA_
not modelled 97.0 13 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
85d1jhfa1
not modelled 96.9 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
86c3v4gA_
not modelled 96.9 15 PDB header:dna binding protein
Chain: A: PDB Molecule:arginine repressor;
PDBTitle: 1.60 angstrom resolution crystal structure of an arginine repressor2 from vibrio vulnificus cmcp6
87d1r1ua_
not modelled 96.9 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
88c3f6vA_
not modelled 96.9 8 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
89c3cdkA_
not modelled 96.9 15 PDB header:transferase
Chain: A: 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
90d2p4wa1
not modelled 96.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
91d2ev0a1
not modelled 96.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
92d1ulya_
not modelled 96.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein PH1932
93d1ub9a_
not modelled 96.9 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
94c3f6oB_
not modelled 96.9 10 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
95c1r22B_
not modelled 96.8 16 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
96c3nzeB_
not modelled 96.8 11 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator, sugar-binding family;
PDBTitle: the crystal structure of a domain of a possible sugar-binding2 transcriptional regulator from arthrobacter aurescens tc1.
97d1f9na1
not modelled 96.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
98c2zkzC_
not modelled 96.7 14 PDB header:transcription
Chain: C: PDB Molecule:transcriptional repressor pagr;
PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
99c3kv1A_
not modelled 96.6 9 PDB header:transcription
Chain: A: PDB Molecule:transcriptional repressor;
PDBTitle: crystal structure of putative sugar-binding domain of transcriptional2 repressor from vibrio fischeri
100d1sfxa_
not modelled 96.6 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
101c3rrlC_
not modelled 96.6 16 PDB header:transferase
Chain: C: PDB Molecule:succinyl-coa:3-ketoacid-coenzyme a transferase subunit a;
PDBTitle: complex structure of 3-oxoadipate coa-transferase subunit a and b from2 helicobacter pylori 26695
102c2kkoB_
not modelled 96.6 18 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.
103d1r1ta_
not modelled 96.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
104c3eh7A_
not modelled 96.6 14 PDB header:transferase
Chain: A: PDB Molecule:4-hydroxybutyrate coa-transferase;
PDBTitle: the structure of a putative 4-hydroxybutyrate coa-transferase from2 porphyromonas gingivalis w83
105c2dt5A_
not modelled 96.5 15 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
106c3jthA_
not modelled 96.5 13 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
107d1mkma1
not modelled 96.4 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
108d2htja1
not modelled 96.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:FaeA-like
109c2ev5B_
not modelled 96.3 13 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
110c2ahvC_
not modelled 96.3 22 PDB header:transferase
Chain: C: PDB Molecule:putative enzyme ydif;
PDBTitle: crystal structure of acyl-coa transferase from e. coli o157:h7 (ydif)-2 thioester complex with coa- 1
111d1okra_
not modelled 96.3 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
112c1mkmA_
not modelled 96.2 8 PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr
113c2nyxB_
not modelled 96.2 16 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
114d3efba1
not modelled 96.1 14 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:SorC sugar-binding domain-like
115c2qwwB_
not modelled 96.1 2 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
116c2jscB_
not modelled 96.1 12 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050;
PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
117d2okga1
not modelled 96.1 13 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:SorC sugar-binding domain-like
118c3eyyA_
not modelled 96.0 14 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
119c3bj6B_
not modelled 96.0 13 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
120d2fxaa1
not modelled 96.0 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators

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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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