Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP24255
DateThu Jan 5 11:41:39 GMT 2012
Unique Job IDfc499dc3c57a84a9

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2k9mA_
Top template information
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: structure of the core binding domain of sigma54
Confidence and coverage
Confidence: 99.9% Coverage: 26%
126 residues ( 26% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
298 residues ( 62%) 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  MKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDTHEEIDTRE
Secondary structure 


























SS confidence 



























































Disorder  ????????????????
































???????????
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   .........70.........80.........90.........100.........110.........120
Sequence  TQDSETLDTADALEQKEMPEELPLDASWDTIYTAGTPSGTSGDYIDDELPVYQGETTQTL
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Disorder  ?????????????????????????






????????????????


??????


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   .........130.........140.........150.........160.........170.........180
Sequence  QDYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVPLEDILESIGDEEIDIDEVEAVLK
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Disorder 









?
















































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   .........190.........200.........210.........220.........230.........240
Sequence  RIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMRVTR
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????






























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   .........250.........260.........270.........280.........290.........300
Sequence  LKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRLQIN
Secondary structure 


























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Disorder 

























???






























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   .........310.........320.........330.........340.........350.........360
Sequence  QHYASMCNNARNDGDSQFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEE
Secondary structure 







SS confidence 



























































Disorder 







?????










































?


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   .........370.........380.........390.........400.........410.........420
Sequence  YMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAI
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Disorder 










































???

?????
?




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   .........430.........440.........450.........460.........470.......
Sequence  RALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV
Secondary structure 





















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Disorder 














??




























???



????
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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 2k9m chain A

3D model

Region: 116 - 263
Aligned: 126
Modelled: 135
Confidence: 99.9%
Identity: 24%
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: structure of the core binding domain of sigma54

Phyre2

PDB 2o8k chain A

3D model

Region: 415 - 474
Aligned: 60
Modelled: 60
Confidence: 99.8%
Identity: 43%
PDB header:transcription/dna
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element

Phyre2

PDB 2k9l chain A

3D model

Region: 108 - 186
Aligned: 75
Modelled: 79
Confidence: 99.4%
Identity: 21%
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: structure of the core binding domain of sigma54

Phyre2

PDB 1lcd chain A

3D model

Region: 362 - 388
Aligned: 27
Modelled: 27
Confidence: 97.3%
Identity: 41%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 2bjc chain A domain 1

3D model

Region: 362 - 388
Aligned: 27
Modelled: 27
Confidence: 97.3%
Identity: 41%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 3kjx chain D

3D model

Region: 363 - 388
Aligned: 26
Modelled: 26
Confidence: 97.1%
Identity: 35%
PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi

Phyre2

PDB 1efa chain A domain 1

3D model

Region: 363 - 388
Aligned: 26
Modelled: 26
Confidence: 97.0%
Identity: 38%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 1uxd chain A

3D model

Region: 365 - 388
Aligned: 24
Modelled: 24
Confidence: 96.8%
Identity: 33%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 1zvv chain A

3D model

Region: 362 - 388
Aligned: 26
Modelled: 27
Confidence: 96.8%
Identity: 27%
PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex

Phyre2

PDB 2hsg chain A domain 1

3D model

Region: 365 - 388
Aligned: 24
Modelled: 24
Confidence: 96.8%
Identity: 25%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 1uxc chain A

3D model

Region: 365 - 388
Aligned: 24
Modelled: 24
Confidence: 96.8%
Identity: 33%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 1bdh chain A

3D model

Region: 366 - 388
Aligned: 23
Modelled: 23
Confidence: 96.6%
Identity: 22%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex

Phyre2

PDB 1qpz chain A domain 1

3D model

Region: 366 - 388
Aligned: 23
Modelled: 23
Confidence: 96.5%
Identity: 22%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: GalR/LacI-like bacterial regulator

Phyre2

PDB 2lcv chain A

3D model

Region: 366 - 388
Aligned: 23
Modelled: 23
Confidence: 96.3%
Identity: 22%
PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional repressor cytr;
PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation

Phyre2

PDB 1u78 chain A

3D model

Region: 365 - 466
Aligned: 82
Modelled: 89
Confidence: 96.3%
Identity: 11%
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

Phyre2

PDB 3h5t chain A

3D model

Region: 363 - 388
Aligned: 26
Modelled: 26
Confidence: 96.3%
Identity: 23%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum

Phyre2

PDB 2l8n chain A

3D model

Region: 366 - 388
Aligned: 23
Modelled: 23
Confidence: 96.2%
Identity: 22%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional repressor cytr;
PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna

Phyre2

PDB 1r71 chain A

3D model

Region: 325 - 465
Aligned: 111
Modelled: 141
Confidence: 95.2%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: KorB DNA-binding domain-like
Family: KorB DNA-binding domain-like

Phyre2

PDB 1r71 chain B

3D model

Region: 325 - 466
Aligned: 113
Modelled: 133
Confidence: 94.8%
Identity: 23%
PDB header:transcription/dna
Chain: B: PDB Molecule:transcriptional repressor protein korb;
PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna

Phyre2

PDB 6pax chain A

3D model

Region: 365 - 459
Aligned: 83
Modelled: 94
Confidence: 94.4%
Identity: 10%
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

Phyre2

PDB 3dkw chain B

3D model

Region: 297 - 386
Aligned: 90
Modelled: 90
Confidence: 93.7%
Identity: 12%
PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.

Phyre2

PDB 3e6d chain A

3D model

Region: 313 - 386
Aligned: 74
Modelled: 74
Confidence: 92.8%
Identity: 19%
PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s

Phyre2

PDB 2fmy chain B

3D model

Region: 322 - 386
Aligned: 65
Modelled: 65
Confidence: 91.0%
Identity: 11%
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)

Phyre2
1

c2k9mA_
2

c2o8kA_
3

c2k9lA_
4

d1lcda_
5

d2bjca1
6

c3kjxD_
7

d1efaa1
8

d1uxda_
9

c1zvvA_
10

d2hsga1
11

d1uxca_
12

c1bdhA_
13

d1qpza1
14

c2lcvA_
15

c1u78A_
16

c3h5tA_
17

c2l8nA_
18

d1r71a_
19

c1r71B_
20

c6paxA_
21



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c3dkwB_
24



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c3e6dA_
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c2fmyB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2k9mA_



99.9 24 PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: structure of the core binding domain of sigma54
2c2o8kA_



99.8 43 PDB header:transcription/dna
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element
3c2k9lA_



99.4 21 PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpon;
PDBTitle: structure of the core binding domain of sigma54
4d1lcda_



97.3 41 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
5d2bjca1



97.3 41 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
6c3kjxD_



97.1 35 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
7d1efaa1



97.0 38 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
8d1uxda_



96.8 33 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
9c1zvvA_



96.8 27 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
10d2hsga1



96.8 25 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
11d1uxca_



96.8 33 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
12c1bdhA_



96.6 22 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
13d1qpza1



96.5 22 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
14c2lcvA_



96.3 22 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional repressor cytr;
PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
15c1u78A_



96.3 11 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
16c3h5tA_



96.3 23 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
17c2l8nA_



96.2 22 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional repressor cytr;
PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna
18d1r71a_



95.2 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
19c1r71B_



94.8 23 PDB header:transcription/dna
Chain: B: PDB Molecule:transcriptional repressor protein korb;
PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna
20c6paxA_



94.4 10 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
21c3mn2B_



not modelled 94.2 15 PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
22d1pdnc_



not modelled 94.2 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
23c3dkwB_



93.7 12 PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.
24d2gaua1



not modelled 93.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
25c3e6dA_



92.8 19 PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s
26d2coha1



not modelled 92.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
27c2fxaB_



not modelled 92.1 11 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
28c3dv8A_



not modelled 92.1 7 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
29c3deuB_



not modelled 92.0 15 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
30c3bj6B_



not modelled 92.0 20 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
31d3e5ua1



not modelled 92.0 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
32c2o3fC_



not modelled 91.7 8 PDB header:transcription
Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh;
PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168.
33d2o3fa1



not modelled 91.7 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:RpiR-like
34d1mkma1



not modelled 91.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
35c3iwfA_



not modelled 91.6 17 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
36d2bgca1



not modelled 91.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
37d1ku9a_



not modelled 91.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
38d1z05a1



not modelled 91.4 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
39d2h6ca1



not modelled 91.3 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
40d1ft9a1



not modelled 91.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
41c2fmyB_



91.0 11 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)
42c2kpjA_



not modelled 90.9 11 PDB header:transcription regulator
Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa;
PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a
43d2a6ca1



not modelled 90.9 12 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
44d2fxaa1



not modelled 90.8 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
45c2gauA_



not modelled 90.7 11 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
46c1b0nA_



not modelled 90.7 17 PDB header:transcription regulator
Chain: A: PDB Molecule:protein (sinr protein);
PDBTitle: sinr protein/sini protein complex
47c3oioA_



not modelled 90.6 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum
48c3r0aB_



not modelled 90.4 13 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
49c1ft9A_



not modelled 90.1 11 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
50d1lmb3_



not modelled 90.1 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
51d1hlva1



not modelled 90.0 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
52c1iufA_



not modelled 89.9 9 PDB header:dna binding protein
Chain: A: PDB Molecule:centromere abp1 protein;
PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein
53c3t76A_



not modelled 89.8 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator vanug;
PDBTitle: crystal structure of transcriptional regulator vanug, form ii
54c3hrmA_



not modelled 89.6 12 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
55d1ttya_



not modelled 89.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
56d2b5aa1



not modelled 89.4 23 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
57d1zs4a1



not modelled 89.4 37 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Bacteriophage CII protein
58d1bw6a_



not modelled 89.0 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
59d2o38a1



not modelled 88.9 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
60c2o38A_



not modelled 88.9 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: putative xre family transcriptional regulator
61d2d1ha1



not modelled 88.8 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
62d2croa_



not modelled 88.7 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
63d1i5za1



not modelled 88.7 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
64c1hlvA_



not modelled 88.7 16 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:major centromere autoantigen b;
PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna
65c1z6rC_



not modelled 88.6 15 PDB header:transcription
Chain: C: PDB Molecule:mlc protein;
PDBTitle: crystal structure of mlc from escherichia coli
66d2oz6a1



not modelled 88.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
67c2g7uB_



not modelled 88.4 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: 2.3 a structure of putative catechol degradative operon regulator from2 rhodococcus sp. rha1
68c3d0sA_



not modelled 88.4 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form
69c1mkmA_



not modelled 88.4 17 PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr
70c2oz6A_



not modelled 88.4 10 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
71c2k27A_



not modelled 88.3 12 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
72d1t56a1



not modelled 88.3 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
73c2ia2D_



not modelled 88.2 25 PDB header:transcription
Chain: D: PDB Molecule:putative transcriptional regulator;
PDBTitle: the crystal structure of a putative transcriptional regulator rha061952 from rhodococcus sp. rha1
74c1zreB_



not modelled 88.1 13 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
75c3omtA_



not modelled 88.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
76c2xroE_



not modelled 88.1 29 PDB header:dna-binding protein/dna
Chain: E: PDB Molecule:hth-type transcriptional regulator ttgv;
PDBTitle: crystal structure of ttgv in complex with its dna operator
77d1y9qa1



not modelled 88.1 7 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
78c2qwwB_



not modelled 88.1 13 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
79c3f6wE_



not modelled 88.0 12 PDB header:dna binding protein
Chain: E: PDB Molecule:xre-family like protein;
PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000
80c3cecA_



not modelled 87.8 21 PDB header:transcription
Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system;
PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
81c3eusB_



not modelled 87.8 25 PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding protein;
PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
82d2p5ka1



not modelled 87.7 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
83d1b0na2



not modelled 87.6 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
84d1b4aa1



not modelled 87.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
85d1y7ya1



not modelled 87.5 13 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
86c1z05A_



not modelled 87.4 20 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, rok family;
PDBTitle: crystal structure of the rok family transcriptional regulator, homolog2 of e.coli mlc protein.
87c2w48D_



not modelled 87.4 35 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
88d1ku3a_



not modelled 87.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
89c1y9qA_



not modelled 87.4 12 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, hth_3 family;
PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
90c3nrgA_



not modelled 87.3 17 PDB header:transcription
Chain: A: PDB Molecule:tetr family transcriptional regulator;
PDBTitle: crystal structure of a tetr family transcriptional regulator2 (caur_2714) from chloroflexus aurantiacus j-10-fl at 2.56 a3 resolution
91c3bs3A_



not modelled 87.3 18 PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna-binding protein;
PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis
92d1utxa_



not modelled 87.3 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
93c3bddD_



not modelled 87.2 9 PDB header:transcription
Chain: D: PDB Molecule:regulatory protein marr;
PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution
94d1z6ra1



not modelled 87.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
95d1pb6a1



not modelled 87.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
96c3oouA_



not modelled 87.2 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua
97c2fd5A_



not modelled 87.2 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: the crystal structure of a transcriptional regulator from pseudomonas2 aeruginosa pao1
98c3iwzB_



not modelled 87.2 9 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
99d1aoya_



not modelled 87.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
100d1lj9a_



not modelled 87.0 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
101c3kccA_



not modelled 86.9 13 PDB header:transcription
Chain: A: PDB Molecule:catabolite gene activator;
PDBTitle: crystal structure of d138l mutant of catabolite gene activator protein
102d2r1jl1



not modelled 86.8 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
103c3pqkD_



not modelled 86.8 20 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
104c2ebyA_



not modelled 86.8 16 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli
105c2zcxA_



not modelled 86.8 30 PDB header:transcription
Chain: A: PDB Molecule:tetr-family transcriptional regulator;
PDBTitle: crystal structure of tetr family transcriptional regulator2 sco7815
106d1f9na1



not modelled 86.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
107c1b4aA_



not modelled 86.7 18 PDB header:repressor
Chain: A: PDB Molecule:arginine repressor;
PDBTitle: structure of the arginine repressor from bacillus stearothermophilus
108c3trbA_



not modelled 86.7 10 PDB header:dna binding protein
Chain: A: PDB Molecule:virulence-associated protein i;
PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii
109d2ofya1



not modelled 86.6 12 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
110d1r69a_



not modelled 86.5 26 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
111d2fx0a1



not modelled 86.4 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
112c3ereD_



not modelled 86.4 25 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
113d2p7vb1



not modelled 86.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
114d1rioa_



not modelled 86.3 8 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
115d2icta1



not modelled 86.2 30 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
116c3mklB_



not modelled 86.1 15 PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
117d1adra_



not modelled 86.1 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
118c2nx4A_



not modelled 86.1 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:transcriptional regulator, tetr family protein;
PDBTitle: the crystal structure of athe putative tetr-family transcriptional2 regulator rha06780 from rhodococcus sp. rha1.
119d1llib_



not modelled 86.1 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
120c3fmyA_



not modelled 86.0 8 PDB header:dna binding protein
Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa
PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021)

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