Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0ACM5
DateThu Jan 5 11:18:32 GMT 2012
Unique Job ID492750c149a7969d

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3bwgA_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage: 88%
217 residues ( 88% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MEQAHTQLIAQLNERILAADNTPLYIKFAETVKNAVRSGVLEHGNILPGERDLSQLTGVS
Secondary structure 
SS confidence 
Disorder  ???
????????
????????
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  RITVRKAMQALEEEGVVTRSRGYGTQINNIFEYSLKEARGFSQQVVLRGKKPDTLWVNKR
Secondary structure 
SS confidence 
Disorder 
?
???????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  VVKCPEEVAQQLAVEAGSDVFLLKRIRYVDEEAVSIEESWVPAHLIHDVDAIGISLYDYF
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  RSQHIYPQRTRSRVSARMPDAEFQSHIQLDSKIPVLVIKQVALDQQQRPIEYSISHCRSD
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   ........
Sequence  LYVFVCEE
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 3bwg chain A

3D model

Region: 26 - 247
Aligned: 217
Modelled: 222
Confidence: 100.0%
Identity: 19%
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

Phyre2

PDB 3edp chain B

3D model

Region: 22 - 247
Aligned: 215
Modelled: 225
Confidence: 100.0%
Identity: 19%
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

Phyre2

PDB 3f8m chain A

3D model

Region: 24 - 247
Aligned: 222
Modelled: 224
Confidence: 100.0%
Identity: 24%
PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis

Phyre2

PDB 3eet chain A

3D model

Region: 21 - 247
Aligned: 226
Modelled: 227
Confidence: 100.0%
Identity: 19%
PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator

Phyre2

PDB 2wv0 chain H

3D model

Region: 15 - 247
Aligned: 216
Modelled: 233
Confidence: 100.0%
Identity: 25%
PDB header:transcription
Chain: H: PDB Molecule:hth-type transcriptional repressor yvoa;
PDBTitle: crystal structure of the gntr-hutc family member yvoa from2 bacillus subtilis

Phyre2

PDB 3f8l chain C

3D model

Region: 93 - 247
Aligned: 155
Modelled: 155
Confidence: 99.9%
Identity: 24%
PDB header:transcription
Chain: C: PDB Molecule:hth-type transcriptional repressor phnf;
PDBTitle: crystal structure of the effector domain of phnf from mycobacterium2 smegmatis

Phyre2

PDB 3by6 chain C

3D model

Region: 14 - 90
Aligned: 77
Modelled: 77
Confidence: 99.9%
Identity: 27%
PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni

Phyre2

PDB 3neu chain A

3D model

Region: 19 - 90
Aligned: 72
Modelled: 72
Confidence: 99.9%
Identity: 25%
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

Phyre2

PDB 2du9 chain A

3D model

Region: 22 - 107
Aligned: 86
Modelled: 86
Confidence: 99.9%
Identity: 21%
PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum

Phyre2

PDB 2fa1 chain A domain 1

3D model

Region: 95 - 247
Aligned: 153
Modelled: 153
Confidence: 99.9%
Identity: 25%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 2p19 chain A domain 1

3D model

Region: 106 - 247
Aligned: 142
Modelled: 142
Confidence: 99.9%
Identity: 25%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 3cnv chain A domain 1

3D model

Region: 104 - 247
Aligned: 144
Modelled: 144
Confidence: 99.9%
Identity: 19%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 2ra5 chain A

3D model

Region: 107 - 247
Aligned: 141
Modelled: 141
Confidence: 99.9%
Identity: 23%
PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator2 from streptomyces coelicolor

Phyre2

PDB 2ra5 chain A domain 1

3D model

Region: 107 - 247
Aligned: 141
Modelled: 141
Confidence: 99.9%
Identity: 23%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 2ooi chain A domain 1

3D model

Region: 96 - 247
Aligned: 152
Modelled: 152
Confidence: 99.9%
Identity: 20%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 1v4r chain A domain 1

3D model

Region: 17 - 113
Aligned: 97
Modelled: 97
Confidence: 99.8%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: GntR-like transcriptional regulators

Phyre2

PDB 3bwg chain A domain 2

3D model

Region: 109 - 247
Aligned: 139
Modelled: 139
Confidence: 99.8%
Identity: 19%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 2di3 chain A

3D model

Region: 23 - 113
Aligned: 91
Modelled: 91
Confidence: 99.8%
Identity: 30%
PDB header:transcription
Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family;
PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum

Phyre2

PDB 2ikk chain A domain 1

3D model

Region: 111 - 247
Aligned: 137
Modelled: 137
Confidence: 99.8%
Identity: 20%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 2ogg chain A domain 1

3D model

Region: 112 - 247
Aligned: 136
Modelled: 136
Confidence: 99.8%
Identity: 17%
Fold: Chorismate lyase-like
Superfamily: Chorismate lyase-like
Family: UTRA domain

Phyre2

PDB 1s3j chain A

3D model

Region: 1 - 82
Aligned: 72
Modelled: 68
Confidence: 95.1%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
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c3bwgA_
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c3edpB_
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c3f8mA_
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c3eetA_
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c2wv0H_
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c3f8lC_
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c3by6C_
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c3neuA_
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c2du9A_
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d2fa1a1
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d2p19a1
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d3cnva1
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c2ra5A_
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d2ra5a1
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d2ooia1
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d1v4ra1
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d3bwga2
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c2di3A_
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d2ikka1
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d2ogga1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3bwgA_
100.0 19 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
2c3edpB_
100.0 19 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
3c3f8mA_
100.0 24 PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis
4c3eetA_
100.0 19 PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
5c2wv0H_
100.0 25 PDB header:transcription
Chain: H: PDB Molecule:hth-type transcriptional repressor yvoa;
PDBTitle: crystal structure of the gntr-hutc family member yvoa from2 bacillus subtilis
6c3f8lC_
99.9 24 PDB header:transcription
Chain: C: PDB Molecule:hth-type transcriptional repressor phnf;
PDBTitle: crystal structure of the effector domain of phnf from mycobacterium2 smegmatis
7c3by6C_
99.9 27 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
8c3neuA_
99.9 25 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
9c2du9A_
99.9 21 PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
10d2fa1a1
99.9 25 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
11d2p19a1
99.9 25 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
12d3cnva1
99.9 19 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
13c2ra5A_
99.9 23 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator2 from streptomyces coelicolor
14d2ra5a1
99.9 23 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
15d2ooia1
99.9 20 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
16d1v4ra1
99.8 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
17d3bwga2
99.8 19 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
18c2di3A_
99.8 30 PDB header:transcription
Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family;
PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
19d2ikka1
99.8 20 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
20d2ogga1
99.8 17 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
21c3c7jA_
not modelled 99.8 23 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
22c1e2xA_
not modelled 99.8 28 PDB header:transcriptional regulation
Chain: A: PDB Molecule:fatty acid metabolism regulator protein;
PDBTitle: fadr, fatty acid responsive transcription factor from e.2 coli
23c3fmsA_
not modelled 99.8 24 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
24c3ihuA_
not modelled 99.8 24 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
25c3hfiA_
not modelled 99.8 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative regulator;
PDBTitle: the crystal structure of the putative regulator from escherichia coli2 cft073
26d3bwga1
not modelled 99.8 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
27c2hs5A_
not modelled 99.8 26 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
28c3ic7A_
not modelled 99.8 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator of gntr family2 from bacteroides thetaiotaomicron
29c3lheA_
not modelled 99.8 21 PDB header:transcription regulator
Chain: A: PDB Molecule:gntr family transcriptional regulator;
PDBTitle: the crystal structure of the c-terminal domain of a gntr2 family transcriptional regulator from bacillus anthracis3 str. sterne
30d1hw1a1
not modelled 99.8 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
31d2pkha1
not modelled 99.8 19 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
32c3tqnC_
not modelled 99.8 22 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: structure of the transcriptional regulator of the gntr family, from2 coxiella burnetii.
33d3ddva1
not modelled 99.8 18 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:UTRA domain
34d2hs5a1
not modelled 99.8 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
35c2h09A_
not modelled 98.2 21 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
36d1biaa1
not modelled 98.2 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
37c1f5tA_
not modelled 97.9 20 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
38d1stza1
not modelled 97.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
39d1jhfa1
not modelled 97.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
40c2it0A_
not modelled 97.7 15 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
41c3hruA_
not modelled 97.6 22 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
42c3ctaA_
not modelled 97.5 20 PDB header:transferase
Chain: A: PDB Molecule:riboflavin kinase;
PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
43d1g3wa1
not modelled 97.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
44d1j5ya1
not modelled 97.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
45c1g3wA_
not modelled 97.4 20 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
46d1i5za1
not modelled 97.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
47d2isya1
not modelled 97.3 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
48c2ewnA_
not modelled 97.3 19 PDB header:ligase, transcription
Chain: A: PDB Molecule:bira bifunctional protein;
PDBTitle: ecoli biotin repressor with co-repressor analog
49c1j5yA_
not modelled 97.2 16 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
50c3r0aB_
not modelled 97.2 24 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
51c1zybA_
not modelled 97.1 15 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator, crp family;
PDBTitle: crystal structure of transcription regulator from bacteroides2 thetaiotaomicron vpi-5482 at 2.15 a resolution
52c3k69A_
not modelled 97.1 16 PDB header:transcription
Chain: A: PDB Molecule:putative transcription regulator;
PDBTitle: crystal structure of a putative transcriptional regulator (lp_0360)2 from lactobacillus plantarum at 1.95 a resolution
53c2y75F_
not modelled 97.1 20 PDB header:transcription
Chain: F: PDB Molecule:hth-type transcriptional regulator cymr;
PDBTitle: the structure of cymr (yrzc) the global cysteine regulator2 of b. subtilis
54c2v79B_
not modelled 96.9 12 PDB header:dna-binding protein
Chain: B: PDB Molecule:dna replication protein dnad;
PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis
55d2h6ca1
not modelled 96.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
56c1fx7C_
not modelled 96.8 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
57c3lwfD_
not modelled 96.8 20 PDB header:transcription regulator
Chain: D: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator (np_470886.1)2 from listeria innocua at 2.06 a resolution
58c2gauA_
not modelled 96.7 10 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator, crp/fnr family from2 porphyromonas gingivalis (apc80792), structural genomics, mcsg
59d1xd7a_
not modelled 96.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator Rrf2
60c2oz6A_
not modelled 96.7 14 PDB header:dna binding protein
Chain: A: PDB Molecule:virulence factor regulator;
PDBTitle: crystal structure of virulence factor regulator from pseudomonas2 aeruginosa in complex with camp
61d1sfxa_
not modelled 96.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
62d2gaua1
not modelled 96.6 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
63c2x4hA_
not modelled 96.6 18 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
64c3iwzB_
not modelled 96.6 10 PDB header:transcription
Chain: B: PDB Molecule:catabolite activation-like protein;
PDBTitle: the c-di-gmp responsive global regulator clp links cell-cell signaling2 to virulence gene expression in xanthomonas campestris
65c3dv8A_
not modelled 96.5 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of a putative transcriptional regulator of the2 crp/fnr family (eubrec_1222) from eubacterium rectale atcc 33656 at3 2.55 a resolution
66d3broa1
not modelled 96.5 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
67d2d1ha1
not modelled 96.5 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
68c1zreB_
not modelled 96.4 16 PDB header:gene regulation/dna
Chain: B: PDB Molecule:catabolite gene activator;
PDBTitle: 4 crystal structures of cap-dna with all base-pair2 substitutions at position 6, cap-[6g;17c]icap38 dna
69d1ft9a1
not modelled 96.4 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
70c3bj6B_
not modelled 96.4 14 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
71d2oz6a1
not modelled 96.4 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
72c3fx3A_
not modelled 96.4 16 PDB header:camp-binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: structure of a putative camp-binding regulatory protein from2 silicibacter pomeroyi dss-3
73c3d0sA_
not modelled 96.4 29 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form
74c3e97A_
not modelled 96.3 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator of crp/fnr2 family (yp_604437.1) from deinococcus geothermalis dsm3 11300 at 1.86 a resolution
75d2coha1
not modelled 96.2 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
76c1ft9A_
not modelled 96.2 23 PDB header:transcription
Chain: A: PDB Molecule:carbon monoxide oxidation system transcription
PDBTitle: structure of the reduced (feii) co-sensing protein from r.2 rubrum
77c3kccA_
not modelled 96.2 15 PDB header:transcription
Chain: A: PDB Molecule:catabolite gene activator;
PDBTitle: crystal structure of d138l mutant of catabolite gene activator protein
78d3e5ua1
not modelled 96.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
79d2fbha1
not modelled 96.1 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
80d2fxaa1
not modelled 96.1 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
81d1ku9a_
not modelled 96.0 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
82c2vn2B_
not modelled 96.0 19 PDB header:replication
Chain: B: PDB Molecule:chromosome replication initiation protein;
PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426
83d3ctaa1
not modelled 96.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
84d2cg4a1
not modelled 96.0 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
85d2bgca1
not modelled 96.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
86c3e6dA_
not modelled 96.0 20 PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s
87d2ev0a1
not modelled 95.9 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
88d1i1ga1
not modelled 95.9 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
89d1dpua_
not modelled 95.9 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:C-terminal domain of RPA32
90c1dpuA_
not modelled 95.9 22 PDB header:dna binding protein
Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain;
PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88)
91c3la2A_
not modelled 95.9 14 PDB header:transcription
Chain: A: PDB Molecule:global nitrogen regulator;
PDBTitle: crystal structure of ntca in complex with 2-oxoglutarate
92c2fmyB_
not modelled 95.9 14 PDB header:dna binding protein
Chain: B: PDB Molecule:carbon monoxide oxidation system transcription regulator
PDBTitle: co-dependent transcription factor cooa from carboxydothermus2 hydrogenoformans (imidazole-bound form)
93c2zcwA_
not modelled 95.8 28 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, fnr/crp family;
PDBTitle: crystal structure of ttha1359, a transcriptional regulator,2 crp/fnr family from thermus thermophilus hb8
94c2ev5B_
not modelled 95.8 16 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
95c2bgcA_
not modelled 95.8 11 PDB header:transcription
Chain: A: PDB Molecule:prfa;
PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes
96d1ylfa1
not modelled 95.7 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator Rrf2
97c2l4aA_
not modelled 95.6 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
98d1mkma1
not modelled 95.6 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
99c2gxgA_
not modelled 95.6 20 PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
100c3k2zA_
not modelled 95.6 15 PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima
101d2cfxa1
not modelled 95.5 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
102c2zdbA_
not modelled 95.5 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp family;
PDBTitle: crystal structure of tthb099, a transcriptional regulator crp family2 from thermus thermophilus hb8
103d2cyya1
not modelled 95.5 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
104d3deua1
not modelled 95.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
105c3dkwB_
not modelled 95.4 11 PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.
106c2qwwB_
not modelled 95.4 15 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
107c2zy3A_
not modelled 95.4 10 PDB header:lyase
Chain: A: PDB Molecule:l-aspartate beta-decarboxylase;
PDBTitle: dodecameric l-aspartate beta-decarboxylase
108c2oqgA_
not modelled 95.4 23 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
109c3nqoB_
not modelled 95.4 16 PDB header:transcription
Chain: B: PDB Molecule:marr-family transcriptional regulator;
PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
110d2bv6a1
not modelled 95.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
111d1p4xa2
not modelled 95.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
112c3f6tA_
not modelled 95.3 18 PDB header:transferase
Chain: A: PDB Molecule:aspartate aminotransferase;
PDBTitle: crystal structure of aspartate aminotransferase (e.c. 2.6.1.1)2 (yp_194538.1) from lactobacillus acidophilus ncfm at 2.15 a3 resolution
113c3tgnA_
not modelled 95.3 26 PDB header:transcription
Chain: A: PDB Molecule:adc operon repressor adcr;
PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state
114d2fbia1
not modelled 95.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
115c3l09B_
not modelled 95.3 20 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator2 (jann_22dec04_contig27_revised_gene3569) from jannaschia sp. ccs1 at3 2.81 a resolution
116d1jgsa_
not modelled 95.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
117d2nwia1
not modelled 95.2 11 Fold:Chorismate lyase-like
Superfamily:Chorismate lyase-like
Family:AF1396-like
118c3f6vA_
not modelled 95.2 24 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
119c1r22B_
not modelled 95.2 24 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
120c3oopA_
not modelled 95.2 15 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

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
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