Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AEM6
DateThu Jan 5 11:23:43 GMT 2012
Unique Job IDdf22428f0bec5028

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: 97%
232 residues ( 97% 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  MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYD
Secondary structure 
SS confidence 
Disorder  ?????????
????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEV
Secondary structure 
SS confidence 
Disorder 
??
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  AERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ
Secondary structure 
SS confidence 
Disorder 
?????????????????
??
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........
Sequence  RVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL
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: 4 - 239
Aligned: 232
Modelled: 233
Confidence: 100.0%
Identity: 25%
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: 5 - 239
Aligned: 224
Modelled: 224
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 1rp3 chain G

3D model

Region: 6 - 239
Aligned: 222
Modelled: 234
Confidence: 100.0%
Identity: 35%
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 3iyd chain F

3D model

Region: 10 - 233
Aligned: 220
Modelled: 224
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: 5 - 146
Aligned: 139
Modelled: 139
Confidence: 99.9%
Identity: 27%
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 1or7 chain A

3D model

Region: 4 - 238
Aligned: 167
Modelled: 172
Confidence: 99.9%
Identity: 23%
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 - 236
Aligned: 167
Modelled: 170
Confidence: 99.9%
Identity: 19%
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 3mzy chain A

3D model

Region: 42 - 238
Aligned: 117
Modelled: 118
Confidence: 99.8%
Identity: 24%
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 1rp3 chain A domain 3

3D model

Region: 6 - 88
Aligned: 83
Modelled: 83
Confidence: 99.8%
Identity: 33%
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: 5 - 89
Aligned: 82
Modelled: 85
Confidence: 99.8%
Identity: 28%
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 1ku2 chain A domain 2

3D model

Region: 5 - 89
Aligned: 82
Modelled: 82
Confidence: 99.8%
Identity: 28%
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: 10 - 86
Aligned: 74
Modelled: 77
Confidence: 99.7%
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 1smy chain F domain 2

3D model

Region: 147 - 238
Aligned: 91
Modelled: 92
Confidence: 99.5%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1rp3 chain A domain 2

3D model

Region: 168 - 238
Aligned: 71
Modelled: 71
Confidence: 99.5%
Identity: 45%
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: 164 - 238
Aligned: 75
Modelled: 75
Confidence: 99.5%
Identity: 17%
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 1or7 chain A domain 1

3D model

Region: 173 - 238
Aligned: 66
Modelled: 66
Confidence: 99.3%
Identity: 29%
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 2

3D model

Region: 3 - 97
Aligned: 89
Modelled: 95
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 1or7 chain B domain 2

3D model

Region: 3 - 88
Aligned: 80
Modelled: 86
Confidence: 99.3%
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 1ku7 chain A

3D model

Region: 180 - 238
Aligned: 59
Modelled: 59
Confidence: 99.2%
Identity: 29%
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: 176 - 233
Aligned: 58
Modelled: 58
Confidence: 99.2%
Identity: 17%
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
1
c2a6eF_
2
c1l9uH_
3
c1rp3G_
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c3iydF_
5
c1ku2A_
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c1or7A_
7
c2q1zA_
8
c3mzyA_
9
d1rp3a3
10
d1smyf3
11
d1ku2a2
12
d1siga_
13
d1smyf2
14
d1rp3a2
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c3hugA_
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d1or7a1
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d1or7a2
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d1or7b2
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d1ku7a_
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c2o8xA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2a6eF_
100.0 25 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
3c1rp3G_
100.0 35 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
4c3iydF_
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
5c1ku2A_
99.9 27 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
6c1or7A_
99.9 23 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
7c2q1zA_
99.9 19 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
8c3mzyA_
99.8 24 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
9d1rp3a3
99.8 33 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
10d1smyf3
99.8 28 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
11d1ku2a2
99.8 28 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
12d1siga_
99.7 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
13d1smyf2
99.5 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
14d1rp3a2
99.5 45 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
15c3hugA_
99.5 17 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
16d1or7a1
99.3 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
17d1or7a2
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
18d1or7b2
99.3 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
19d1ku7a_
99.2 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
20c2o8xA_
99.2 17 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
21d1xsva_
not modelled 99.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
22c3t72o_
not modelled 99.1 25 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
23d1ttya_
not modelled 99.1 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
24d1s7oa_
not modelled 99.1 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
25d1ku3a_
not modelled 99.1 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
26c2o7gA_
not modelled 99.1 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
27d2p7vb1
not modelled 99.0 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
28d1h3la_
not modelled 98.8 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
29c3n0rA_
not modelled 98.5 16 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 98.5 24 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)
31c3qp5C_
not modelled 98.4 22 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
32c3sztB_
not modelled 98.3 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
33c2q0oA_
not modelled 98.3 18 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 98.2 26 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
35c1x3uA_
not modelled 98.2 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
36c1zljE_
not modelled 98.1 26 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
37d1a04a1
not modelled 98.1 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)
38c2krfB_
not modelled 98.0 21 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
39d1l3la1
not modelled 98.0 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)
40c2rnjA_
not modelled 98.0 26 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
41d1p4wa_
not modelled 98.0 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)
42c3c3wB_
not modelled 98.0 27 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
43d1fsea_
not modelled 98.0 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)
44c3cloC_
not modelled 97.9 33 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
45c3klnC_
not modelled 97.8 25 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
46c1zn2A_
not modelled 97.7 21 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
47c1rnlA_
not modelled 97.7 30 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
48c2jpcA_
not modelled 97.6 25 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
49d1rp3a1
not modelled 97.4 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
50c1u78A_
not modelled 97.1 13 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
51c1l0oC_
not modelled 96.9 30 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
52d1l0oc_
not modelled 96.9 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
53d1ku2a1
not modelled 96.8 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
54c2vbzA_
not modelled 96.5 12 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
55d2cg4a1
not modelled 96.4 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
56d1pdnc_
not modelled 96.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
57c2dbbA_
not modelled 96.3 14 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
58d2cfxa1
not modelled 96.3 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
59c6paxA_
not modelled 96.3 16 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
60c2cg4B_
not modelled 96.2 7 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
61c2p6tH_
not modelled 96.2 16 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
62c2ia0A_
not modelled 96.2 19 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)
63c2cfxD_
not modelled 96.1 14 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
64d1i1ga1
not modelled 95.9 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
65c2e7xA_
not modelled 95.9 19 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
66c2w7nA_
not modelled 95.9 9 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
67c2l4aA_
not modelled 95.9 7 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
68c2e1cA_
not modelled 95.8 19 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
69d2cyya1
not modelled 95.8 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
70d2d1ha1
not modelled 95.8 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
71c1i1gA_
not modelled 95.8 21 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
72c2elhA_
not modelled 95.6 16 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
73c3i4pA_
not modelled 95.6 5 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
74d1k78a1
not modelled 95.5 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
75d1r1ua_
not modelled 95.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
76c3pqkD_
not modelled 95.3 10 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
77c3hyiA_
not modelled 95.2 21 PDB header:transcription regulator
Chain: A: PDB Molecule:protein duf199/whia;
PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima
78d1ku9a_
not modelled 95.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
79c3jthA_
not modelled 95.0 23 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
80c3nqoB_
not modelled 94.9 16 PDB header:transcription
Chain: B: PDB Molecule:marr-family transcriptional regulator;
PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
81c1r22B_
not modelled 94.8 22 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
82c2r0qF_
not modelled 94.7 8 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
83d2o38a1
not modelled 94.7 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
84c2o38A_
not modelled 94.7 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: putative xre family transcriptional regulator
85c3tgnA_
not modelled 94.5 23 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
86c2wteB_
not modelled 94.5 14 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.
87c3r0aB_
not modelled 94.4 13 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
88c3iwfA_
not modelled 94.4 16 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
89c2x4hA_
not modelled 94.2 26 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
90d1vz0a1
not modelled 94.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
91c2gqqB_
not modelled 94.0 7 PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
92d2jn6a1
not modelled 94.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
93d1hlva1
not modelled 94.0 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
94d1r1ta_
not modelled 93.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
95c2oqgA_
not modelled 93.8 12 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
96d1rioa_
not modelled 93.6 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
97d1sfxa_
not modelled 93.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
98d6paxa1
not modelled 93.6 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
99d1jhfa1
not modelled 93.5 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
100c3cuoB_
not modelled 93.1 10 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
101d1biaa1
not modelled 93.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
102d1lmb3_
not modelled 92.9 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
103c1kgsA_
not modelled 92.9 15 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
104c2gxgA_
not modelled 92.9 10 PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
105c1hlvA_
not modelled 92.8 23 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
106d2p4wa1
not modelled 92.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
107c3gn5B_
not modelled 92.7 10 PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
108c2gm4B_
not modelled 92.7 16 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
109c3f6oB_
not modelled 92.6 8 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
110c2x48B_
not modelled 92.6 17 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
111c2da4A_
not modelled 92.5 16 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
112c2kkoB_
not modelled 92.4 18 PDB header:dna binding protein
Chain: B: PDB Molecule:possible transcriptional regulatory protein
PDBTitle: solution nmr structure of the homodimeric winged helix-turn-2 helix dna-binding domain (fragment 1-100) mb0332 from3 mycobacterium bovis, a possible arsr-family transcriptional4 regulator. northeast structural genomics consortium target5 mbr242e.
113c2fa5B_
not modelled 92.3 16 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
114d1lnwa_
not modelled 92.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
115d2fxaa1
not modelled 92.3 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
116d1uxca_
not modelled 92.3 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
117d1jhga_
not modelled 92.1 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
118c2jscB_
not modelled 92.1 17 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050;
PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
119c2k27A_
not modelled 92.0 21 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
120c3kp3B_
not modelled 92.0 14 PDB header:transcription regulator/antibiotic
Chain: B: PDB Molecule:transcriptional regulator tcar;
PDBTitle: staphylococcus epidermidis in complex with ampicillin

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