Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP23484
DateThu Jan 5 11:39:30 GMT 2012
Unique Job IDae20cf7038edd833

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1or7A_
Top template information
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
Confidence and coverage
Confidence: 99.9% Coverage: 97%
167 residues ( 97% of your sequence) have been modelled with 99.9% 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  MSDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRD
Secondary structure 












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Disorder  ??


??












































???????
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   .........70.........80.........90.........100.........110.........120
Sequence  PRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDG
Secondary structure 








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Disorder 

























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   .........130.........140.........150.........160.........170...
Sequence  LNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHCLLFRLEYGL
Secondary structure 











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Disorder 
















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????
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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 1or7 chain A

3D model

Region: 1 - 168
Aligned: 167
Modelled: 167
Confidence: 99.9%
Identity: 19%
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: 1 - 168
Aligned: 167
Modelled: 168
Confidence: 99.9%
Identity: 14%
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 G

3D model

Region: 8 - 171
Aligned: 164
Modelled: 164
Confidence: 99.9%
Identity: 16%
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 3mzy chain A

3D model

Region: 39 - 172
Aligned: 117
Modelled: 117
Confidence: 99.7%
Identity: 17%
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 2a6e chain F

3D model

Region: 2 - 172
Aligned: 170
Modelled: 171
Confidence: 99.6%
Identity: 14%
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: 2 - 173
Aligned: 172
Modelled: 172
Confidence: 99.6%
Identity: 16%
PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution

Phyre2

PDB 1or7 chain A domain 2

3D model

Region: 1 - 101
Aligned: 100
Modelled: 101
Confidence: 99.5%
Identity: 15%
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 B domain 2

3D model

Region: 1 - 82
Aligned: 81
Modelled: 82
Confidence: 99.5%
Identity: 16%
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 2o7g chain A

3D model

Region: 1 - 78
Aligned: 77
Modelled: 78
Confidence: 99.4%
Identity: 25%
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

Phyre2

PDB 3hug chain A

3D model

Region: 96 - 173
Aligned: 78
Modelled: 78
Confidence: 99.4%
Identity: 23%
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 3iyd chain F

3D model

Region: 1 - 166
Aligned: 166
Modelled: 166
Confidence: 99.3%
Identity: 12%
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 1h3l chain A

3D model

Region: 5 - 78
Aligned: 74
Modelled: 74
Confidence: 99.3%
Identity: 20%
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 1rp3 chain A domain 2

3D model

Region: 100 - 170
Aligned: 71
Modelled: 71
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 1or7 chain A domain 1

3D model

Region: 107 - 168
Aligned: 62
Modelled: 62
Confidence: 99.1%
Identity: 27%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 2o8x chain A

3D model

Region: 108 - 165
Aligned: 58
Modelled: 58
Confidence: 99.1%
Identity: 34%
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

Phyre2

PDB 1s7o chain A

3D model

Region: 109 - 173
Aligned: 65
Modelled: 65
Confidence: 99.1%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: YlxM/p13-like

Phyre2

PDB 1xsv chain A

3D model

Region: 104 - 173
Aligned: 70
Modelled: 70
Confidence: 99.1%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: YlxM/p13-like

Phyre2

PDB 3n0r chain A

3D model

Region: 13 - 165
Aligned: 129
Modelled: 129
Confidence: 99.0%
Identity: 16%
PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr stress response regulator at 1.25 angstrom2 resolution

Phyre2

PDB 1smy chain F domain 2

3D model

Region: 91 - 170
Aligned: 79
Modelled: 80
Confidence: 98.9%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1tty chain A

3D model

Region: 113 - 173
Aligned: 61
Modelled: 61
Confidence: 98.8%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2
1

c1or7A_
2

c2q1zA_
3

c1rp3G_
4

c3mzyA_
5

c2a6eF_
6

c1l9uH_
7

d1or7a2
8

d1or7b2
9

c2o7gA_
10

c3hugA_
11

c3iydF_
12

d1h3la_
13

d1rp3a2
14

d1or7a1
15

c2o8xA_
16

d1s7oa_
17

d1xsva_
18

c3n0rA_
19

d1smyf2
20

d1ttya_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1or7A_



99.9 19 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
2c2q1zA_



99.9 14 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
3c1rp3G_



99.9 16 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
4c3mzyA_



99.7 17 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
5c2a6eF_



99.6 14 PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
6c1l9uH_



99.6 16 PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
7d1or7a2



99.5 15 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
8d1or7b2



99.5 16 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
9c2o7gA_



99.4 25 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
10c3hugA_



99.4 23 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
11c3iydF_



99.3 12 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
12d1h3la_



99.3 20 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
13d1rp3a2



99.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
14d1or7a1



99.1 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
15c2o8xA_



99.1 34 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
16d1s7oa_



99.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
17d1xsva_



99.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
18c3n0rA_



99.0 16 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr stress response regulator at 1.25 angstrom2 resolution
19d1smyf2



98.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
20d1ttya_



98.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
21d1ku7a_



not modelled 98.7 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
22d1ku3a_



not modelled 98.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
23d1rp3a3



not modelled 98.7 16 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
24d2p7vb1



not modelled 98.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
25c3t72o_



not modelled 98.5 14 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
26c1ku2A_



not modelled 98.3 15 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
27d1yioa1



not modelled 98.2 25 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)
28c3qp5C_



not modelled 97.9 25 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
29c3sztB_



not modelled 97.9 26 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
30c1x3uA_



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
31d1a04a1



not modelled 97.9 26 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)
32c2rnjA_



not modelled 97.8 24 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
33c2q0oA_



not modelled 97.8 22 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
34c1h0mD_



not modelled 97.8 27 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
35c1zljE_



not modelled 97.8 30 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
36c2krfB_



not modelled 97.8 22 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
37d1p4wa_



not modelled 97.7 26 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)
38d1l3la1



not modelled 97.6 28 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)
39d1fsea_



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)
40c3cloC_



not modelled 97.6 23 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
41c3c3wB_



not modelled 97.5 29 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
42c3klnC_



not modelled 97.4 26 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
43d1smyf3



not modelled 97.3 9 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
44d1ku2a2



not modelled 97.3 9 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
45c2jpcA_



not modelled 97.3 25 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
46c1rnlA_



not modelled 97.2 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
47c1zn2A_



not modelled 97.2 26 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
48d1siga_



not modelled 96.7 9 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
49c1u78A_



not modelled 96.6 18 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
50c6paxA_



not modelled 96.2 23 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
51d1pdnc_



not modelled 96.2 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
52c2cfxD_



not modelled 96.0 21 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
53c2cg4B_



not modelled 95.7 21 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
54c2vbzA_



not modelled 95.7 31 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
55c2dbbA_



not modelled 95.7 18 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
56d2cg4a1



not modelled 95.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
57d1k78a1



not modelled 95.4 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
58c2p6tH_



not modelled 95.2 18 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
59d2cfxa1



not modelled 95.2 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
60c2elhA_



not modelled 95.1 14 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
61c2ia0A_



not modelled 94.9 28 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)
62d1i1ga1



not modelled 94.9 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
63c1i1gA_



not modelled 94.8 28 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
64c2e1cA_



not modelled 94.8 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
65c2e7xA_



not modelled 94.7 14 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
66d1trra_



not modelled 94.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
67c3i4pA_



not modelled 94.6 24 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
68c2l4aA_



not modelled 94.5 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
69d2cyya1



not modelled 94.4 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
70d6paxa1



not modelled 94.4 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
71d1jhga_



not modelled 94.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
72d2jn6a1



not modelled 94.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
73d2d1ha1



not modelled 93.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
74c3frwF_



not modelled 93.4 24 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
75c2gqqB_



not modelled 93.1 21 PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
76c3korD_



not modelled 93.1 21 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
77c2w7nA_



not modelled 93.0 20 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
78d1biaa1



not modelled 92.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
79d1r1ua_



not modelled 92.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
80c2k27A_



not modelled 92.7 23 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
81c1r22B_



not modelled 92.3 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
82c2gm4B_



not modelled 92.3 26 PDB header:recombination, dna
Chain: B: PDB Molecule:transposon gamma-delta resolvase;
PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
83c2r0qF_



not modelled 92.2 16 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
84d1uxca_



not modelled 92.0 33 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
85d1hlva1



not modelled 92.0 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
86c2da4A_



not modelled 91.6 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein dkfzp686k21156;
PDBTitle: solution structure of the homeobox domain of the2 hypothetical protein, dkfzp686k21156
87c2oqgA_



not modelled 91.6 19 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
88c2rn7A_



not modelled 91.3 23 PDB header:unknown function
Chain: A: PDB Molecule:is629 orfa;
PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125
89c3r0aB_



not modelled 91.3 13 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
90d2hsga1



not modelled 91.2 22 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
91d1vz0a1



not modelled 91.1 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
92c3nqoB_



not modelled 90.9 21 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
93c3tgnA_



not modelled 90.9 30 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
94d1rr7a_



not modelled 90.8 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Middle operon regulator, Mor
95c1rr7A_



not modelled 90.8 21 PDB header:transcription
Chain: A: PDB Molecule:middle operon regulator;
PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu
96d2r5yb1



not modelled 90.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
97c2wteB_



not modelled 90.7 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.
98d1jhfa1



not modelled 90.7 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
99d1uxda_



not modelled 90.5 31 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
100d1r1ta_



not modelled 90.5 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
101d1qpza1



not modelled 90.2 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
102d1lcda_



not modelled 89.8 26 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
103c1hlvA_



not modelled 89.3 13 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
104c3cuoB_



not modelled 89.1 16 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
105d2p4wa1



not modelled 89.0 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
106c1kgsA_



not modelled 89.0 13 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
107c2x4hA_



not modelled 88.8 26 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
108c3pvpA_



not modelled 88.8 16 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna
109c2kkoB_



not modelled 88.7 14 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.
110d1r71a_



not modelled 88.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
111c2lk2A_



not modelled 88.3 13 PDB header:transcription
Chain: A: PDB Molecule:homeobox protein tgif1;
PDBTitle: solution nmr structure of homeobox domain (171-248) of human homeobox2 protein tgif1, northeast structural genomics consortium target3 hr4411b
112c3jthA_



not modelled 88.2 14 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
113d1efaa1



not modelled 88.2 26 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
114c1r71B_



not modelled 88.2 16 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
115c3f6oB_



not modelled 87.8 19 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
116d2bjca1



not modelled 87.7 31 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
117d1j5ya1



not modelled 87.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
118d1ku9a_



not modelled 87.5 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
119c2zkzC_



not modelled 87.4 16 PDB header:transcription
Chain: C: PDB Molecule:transcriptional repressor pagr;
PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
120c2l8nA_



not modelled 87.4 26 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

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