Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AGB3
DateThu Jan 5 11:28:39 GMT 2012
Unique Job ID512bff9a879987a3

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2a6eF_
Top template information
PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
Confidence and coverage
Confidence:100.0% Coverage: 93%
263 residues ( 93% 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  MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF
Secondary structure 
SS confidence 
Disorder  ???????????????
?
???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN
Secondary structure 
SS confidence 
Disorder 
?
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARELGVTSKDVREMESRMAAQDM
Secondary structure 
SS confidence 
Disorder 
????????
?
????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  TFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDII
Secondary structure 
SS confidence 
Disorder  ???
???????????
?
?????
Disorder confidence 
 
   .........250.........260.........270.........280....
Sequence  RARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA
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 2a6e chain F

3D model

Region: 10 - 282
Aligned: 263
Modelled: 269
Confidence: 100.0%
Identity: 26%
PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme

Phyre2

PDB 1l9u chain H

3D model

Region: 13 - 282
Aligned: 255
Modelled: 255
Confidence: 100.0%
Identity: 27%
PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution

Phyre2

PDB 3iyd chain F

3D model

Region: 16 - 284
Aligned: 261
Modelled: 269
Confidence: 100.0%
Identity: 25%
PDB header:transcription/dna
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex

Phyre2

PDB 1ku2 chain A

3D model

Region: 16 - 181
Aligned: 166
Modelled: 166
Confidence: 100.0%
Identity: 28%
PDB header:transcription
Chain: A: PDB Molecule:sigma factor siga;
PDBTitle: crystal structure of thermus aquaticus rna polymerase sigma2 subunit fragment containing regions 1.2 to 3.1

Phyre2

PDB 1rp3 chain G

3D model

Region: 44 - 284
Aligned: 217
Modelled: 223
Confidence: 100.0%
Identity: 24%
PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm

Phyre2

PDB 1ku2 chain A domain 2

3D model

Region: 16 - 123
Aligned: 107
Modelled: 108
Confidence: 100.0%
Identity: 45%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1smy chain F domain 3

3D model

Region: 16 - 123
Aligned: 108
Modelled: 108
Confidence: 100.0%
Identity: 36%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1sig chain A

3D model

Region: 16 - 120
Aligned: 104
Modelled: 105
Confidence: 99.9%
Identity: 31%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1or7 chain A

3D model

Region: 33 - 283
Aligned: 173
Modelled: 179
Confidence: 99.9%
Identity: 21%
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma-e factor;
PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea

Phyre2

PDB 2q1z chain A

3D model

Region: 30 - 282
Aligned: 175
Modelled: 179
Confidence: 99.9%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr

Phyre2

PDB 1rp3 chain A domain 3

3D model

Region: 44 - 122
Aligned: 79
Modelled: 79
Confidence: 99.8%
Identity: 30%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 3mzy chain A

3D model

Region: 76 - 283
Aligned: 116
Modelled: 120
Confidence: 99.7%
Identity: 22%
PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a

Phyre2

PDB 1or7 chain B domain 2

3D model

Region: 33 - 122
Aligned: 86
Modelled: 90
Confidence: 99.4%
Identity: 19%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1or7 chain A domain 2

3D model

Region: 33 - 125
Aligned: 89
Modelled: 93
Confidence: 99.4%
Identity: 19%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 3t72 chain O

3D model

Region: 214 - 284
Aligned: 71
Modelled: 71
Confidence: 99.4%
Identity: 31%
PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex

Phyre2

PDB 1smy chain F domain 2

3D model

Region: 190 - 282
Aligned: 86
Modelled: 89
Confidence: 99.3%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 3hug chain A

3D model

Region: 207 - 283
Aligned: 74
Modelled: 77
Confidence: 99.3%
Identity: 15%
PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl

Phyre2

PDB 1rp3 chain A domain 2

3D model

Region: 211 - 283
Aligned: 70
Modelled: 73
Confidence: 99.3%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1ku7 chain A

3D model

Region: 225 - 283
Aligned: 59
Modelled: 59
Confidence: 99.3%
Identity: 34%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1ku3 chain A

3D model

Region: 225 - 282
Aligned: 58
Modelled: 58
Confidence: 99.2%
Identity: 34%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2
1
c2a6eF_
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c1l9uH_
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c3iydF_
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c1ku2A_
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c1rp3G_
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d1ku2a2
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d1smyf3
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d1siga_
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c1or7A_
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c2q1zA_
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d1rp3a3
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c3mzyA_
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d1or7b2
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d1or7a2
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c3t72o_
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d1smyf2
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c3hugA_
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d1rp3a2
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d1ku7a_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2a6eF_
100.0 26 PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
2c1l9uH_
100.0 27 PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
3c3iydF_
100.0 25 PDB header:transcription/dna
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex
4c1ku2A_
100.0 28 PDB header:transcription
Chain: A: PDB Molecule:sigma factor siga;
PDBTitle: crystal structure of thermus aquaticus rna polymerase sigma2 subunit fragment containing regions 1.2 to 3.1
5c1rp3G_
100.0 24 PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm
6d1ku2a2
100.0 45 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
7d1smyf3
100.0 36 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
8d1siga_
99.9 31 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
9c1or7A_
99.9 21 PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma-e factor;
PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea
10c2q1zA_
99.9 20 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
11d1rp3a3
99.8 30 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
12c3mzyA_
99.7 22 PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
13d1or7b2
99.4 19 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
14d1or7a2
99.4 19 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
15c3t72o_
99.4 31 PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex
16d1smyf2
99.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
17c3hugA_
99.3 15 PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
18d1rp3a2
99.3 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
19d1ku7a_
99.3 34 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
20d1ku3a_
99.2 34 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
21c2o7gA_
not modelled 99.2 18 PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the pribnow box recognition region of sigc from2 mycobacterium tuberculosis
22d1ttya_
not modelled 99.2 31 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
23d1or7a1
not modelled 99.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
24d2p7vb1
not modelled 99.1 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
25d1xsva_
not modelled 98.9 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
26c2o8xA_
not modelled 98.9 14 PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
27d1s7oa_
not modelled 98.9 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
28d1h3la_
not modelled 98.7 14 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
29c3n0rA_
not modelled 98.3 15 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr stress response regulator at 1.25 angstrom2 resolution
30d1yioa1
not modelled 98.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
31d1l0oc_
not modelled 98.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
32c1l0oC_
not modelled 98.1 18 PDB header:protein binding
Chain: C: PDB Molecule:sigma factor;
PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf
33c3qp5C_
not modelled 98.1 20 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
34c2q0oA_
not modelled 97.9 24 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
35c3sztB_
not modelled 97.9 23 PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone
36c1h0mD_
not modelled 97.9 30 PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna
37c1x3uA_
not modelled 97.9 23 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
38c1zljE_
not modelled 97.9 22 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
39d1a04a1
not modelled 97.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
40c2krfB_
not modelled 97.7 26 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
41d1ku2a1
not modelled 97.6 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
42d1fsea_
not modelled 97.6 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
43d1l3la1
not modelled 97.6 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
44c2rnjA_
not modelled 97.6 24 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
45d1p4wa_
not modelled 97.5 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
46c3cloC_
not modelled 97.5 28 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution
47c3c3wB_
not modelled 97.4 22 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
48d1rp3a1
not modelled 97.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
49c3klnC_
not modelled 97.3 34 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
50c1zn2A_
not modelled 97.1 18 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
51c2jpcA_
not modelled 97.0 23 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
52c1rnlA_
not modelled 96.9 23 PDB header:signal transduction protein
Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl;
PDBTitle: the nitrate/nitrite response regulator protein narl from narl
53c1u78A_
not modelled 96.5 21 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
54d2d1ha1
not modelled 96.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
55c3r0aB_
not modelled 96.1 11 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
56c3nqoB_
not modelled 95.7 18 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
57d3broa1
not modelled 95.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
58d2cg4a1
not modelled 95.4 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
59d2cfxa1
not modelled 95.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
60d1ku9a_
not modelled 95.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
61c2vbzA_
not modelled 95.4 30 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
62d1jhfa1
not modelled 95.0 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
63c2dbbA_
not modelled 95.0 20 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
64d1pdnc_
not modelled 95.0 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
65c6paxA_
not modelled 94.9 13 PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
66c2l4aA_
not modelled 94.9 20 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
67c2cg4B_
not modelled 94.8 23 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
68c2ia0A_
not modelled 94.8 20 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)
69c2cfxD_
not modelled 94.7 23 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
70c2p6tH_
not modelled 94.6 20 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
71d1i1ga1
not modelled 94.6 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
72d2cyya1
not modelled 94.6 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
73c2e7xA_
not modelled 94.5 23 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
74c2x4hA_
not modelled 94.3 13 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
75c2wteB_
not modelled 94.2 11 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.
76c1i1gA_
not modelled 94.2 30 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
77d1stza1
not modelled 94.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
78c2e1cA_
not modelled 94.1 23 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
79c3iwfA_
not modelled 94.0 15 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator rpir family;
PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
80c3hyiA_
not modelled 94.0 14 PDB header:transcription regulator
Chain: A: PDB Molecule:protein duf199/whia;
PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima
81c2w7nA_
not modelled 94.0 14 PDB header:transcription/dna
Chain: A: PDB Molecule:trfb transcriptional repressor protein;
PDBTitle: crystal structure of kora bound to operator dna: insight2 into repressor cooperation in rp4 gene regulation
82c1r22B_
not modelled 93.8 19 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
83d1k78a1
not modelled 93.7 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
84c3jthA_
not modelled 93.7 18 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
85c3i4pA_
not modelled 93.5 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
86c2elhA_
not modelled 93.5 27 PDB header:dna binding protein
Chain: A: PDB Molecule:cg11849-pa;
PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa
87d1r1ta_
not modelled 93.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
88d2ao9a1
not modelled 93.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
89d1r1ua_
not modelled 93.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
90d1biaa1
not modelled 93.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
91d1hlva1
not modelled 93.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
92c3tgnA_
not modelled 93.1 27 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
93c3cuoB_
not modelled 93.0 15 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
94c3pqkD_
not modelled 92.9 11 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
95c3deuB_
not modelled 92.9 11 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator slya;
PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands
96c2pexA_
not modelled 92.8 12 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator ohrr;
PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris
97d1lnwa_
not modelled 92.8 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
98c2it0A_
not modelled 92.7 17 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
99c1kgsA_
not modelled 92.7 22 PDB header:dna binding protein
Chain: A: PDB Molecule:dna binding response regulator d;
PDBTitle: crystal structure at 1.50 a of an ompr/phob homolog from thermotoga2 maritima
100d1sfxa_
not modelled 92.7 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
101c2qwwB_
not modelled 92.4 8 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
102d1vz0a1
not modelled 92.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
103d1p4xa2
not modelled 92.4 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
104d1trra_
not modelled 92.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
105c2nyxB_
not modelled 92.3 10 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
106c2r0qF_
not modelled 92.3 10 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
107c3mkyP_
not modelled 92.2 15 PDB header:dna binding protein/dna
Chain: P: PDB Molecule:protein sopb;
PDBTitle: structure of sopb(155-323)-18mer dna complex, i23 form
108d2fxaa1
not modelled 92.1 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
109c3nrvC_
not modelled 92.1 20 PDB header:transcription regulator
Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family);
PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1
110c2fa5B_
not modelled 92.0 18 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
111c2oqgA_
not modelled 91.9 16 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
112d2frha1
not modelled 91.8 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
113c3g3zA_
not modelled 91.8 9 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
114c3k0lA_
not modelled 91.5 11 PDB header:transcription regulator
Chain: A: PDB Molecule:repressor protein;
PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
115c3bpxB_
not modelled 91.4 8 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of marr
116c3bj6B_
not modelled 91.4 8 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
117c3hrmA_
not modelled 91.4 18 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator sarz;
PDBTitle: crystal structure of staphylococcus aureus protein sarz in sulfenic2 acid form
118c3cjnA_
not modelled 91.3 9 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
119c2kkoB_
not modelled 91.3 9 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.
120d1jhga_
not modelled 91.2 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR

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