Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77688
DateThu Jan 5 12:31:38 GMT 2012
Unique Job IDe8791d9dd8faa756

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c6paxA_
Top template information
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
Confidence and coverage
Confidence: 99.7% Coverage: 89%
109 residues ( 89% of your sequence) have been modelled with 99.7% 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  MLHTANPVIKHKAGLLNLAEELSNVSKACKIMGVSRDTFYRYRELVAEGGVDAQINRSRR
Secondary structure 

















SS confidence 



























































Disorder  ??????









































??



??????
Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  APNLKNRTDEATEQAVVDYAVAFPTHGQHRASNELRKQGVFISDSGVRSVWLLHNLENLK
Secondary structure 




















SS confidence 



























































Disorder  ??????
?















































????
Disorder confidence 



























































 
   ...
Sequence  RRY
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 6pax chain A

3D model

Region: 9 - 120
Aligned: 109
Modelled: 112
Confidence: 99.7%
Identity: 15%
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 1pdn chain C

3D model

Region: 9 - 111
Aligned: 100
Modelled: 103
Confidence: 99.6%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 1u78 chain A

3D model

Region: 2 - 115
Aligned: 103
Modelled: 114
Confidence: 99.6%
Identity: 14%
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 2k27 chain A

3D model

Region: 9 - 112
Aligned: 101
Modelled: 104
Confidence: 99.5%
Identity: 15%
PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain

Phyre2

PDB 3hos chain A

3D model

Region: 9 - 123
Aligned: 104
Modelled: 105
Confidence: 99.3%
Identity: 11%
PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg

Phyre2

PDB 2jn6 chain A domain 1

3D model

Region: 1 - 83
Aligned: 74
Modelled: 74
Confidence: 98.5%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Cgl2762-like

Phyre2

PDB 1hlv chain A

3D model

Region: 9 - 115
Aligned: 107
Modelled: 107
Confidence: 98.5%
Identity: 8%
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

Phyre2

PDB 1k78 chain A domain 1

3D model

Region: 9 - 50
Aligned: 42
Modelled: 42
Confidence: 98.5%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 6pax chain A domain 1

3D model

Region: 9 - 50
Aligned: 42
Modelled: 42
Confidence: 98.4%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 2rn7 chain A

3D model

Region: 1 - 50
Aligned: 50
Modelled: 50
Confidence: 97.9%
Identity: 10%
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

Phyre2

PDB 2elh chain A

3D model

Region: 9 - 44
Aligned: 36
Modelled: 36
Confidence: 97.2%
Identity: 11%
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

Phyre2

PDB 1ntc chain A

3D model

Region: 7 - 46
Aligned: 40
Modelled: 40
Confidence: 97.1%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2

PDB 1iuf chain A

3D model

Region: 1 - 117
Aligned: 117
Modelled: 117
Confidence: 97.0%
Identity: 13%
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

Phyre2

PDB 1umq chain A

3D model

Region: 8 - 46
Aligned: 39
Modelled: 39
Confidence: 96.9%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2

PDB 1umq chain A

3D model

Region: 8 - 46
Aligned: 39
Modelled: 39
Confidence: 96.9%
Identity: 15%
PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity

Phyre2

PDB 3hef chain B

3D model

Region: 2 - 49
Aligned: 46
Modelled: 48
Confidence: 96.8%
Identity: 17%
PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit

Phyre2

PDB 1fip chain A

3D model

Region: 8 - 46
Aligned: 39
Modelled: 39
Confidence: 96.8%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2

PDB 2r0q chain F

3D model

Region: 5 - 46
Aligned: 42
Modelled: 42
Confidence: 96.7%
Identity: 21%
PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex

Phyre2

PDB 1hlv chain A domain 1

3D model

Region: 9 - 44
Aligned: 36
Modelled: 36
Confidence: 96.6%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Centromere-binding

Phyre2

PDB 1etx chain A

3D model

Region: 8 - 46
Aligned: 39
Modelled: 39
Confidence: 96.6%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
1

c6paxA_
2

d1pdnc_
3

c1u78A_
4

c2k27A_
5

c3hosA_
6

d2jn6a1
7

c1hlvA_
8

d1k78a1
9

d6paxa1
10

c2rn7A_
11

c2elhA_
12

d1ntca_
13

c1iufA_
14

d1umqa_
15

c1umqA_
16

c3hefB_
17

d1fipa_
18

c2r0qF_
19

d1hlva1
20

d1etxa_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c6paxA_



99.7 15 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
2d1pdnc_



99.6 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
3c1u78A_



99.6 14 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
4c2k27A_



99.5 15 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
5c3hosA_



99.3 11 PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
6d2jn6a1



98.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
7c1hlvA_



98.5 8 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
8d1k78a1



98.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
9d6paxa1



98.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
10c2rn7A_



97.9 10 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
11c2elhA_



97.2 11 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
12d1ntca_



97.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
13c1iufA_



97.0 13 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
14d1umqa_



96.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
15c1umqA_



96.9 15 PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
16c3hefB_



96.8 17 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
17d1fipa_



96.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
18c2r0qF_



96.7 21 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
19d1hlva1



96.6 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
20d1etxa_



96.6 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
21c2gm4B_



not modelled 96.6 25 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
22c3e7lD_



not modelled 96.5 13 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
23c2oqgA_



not modelled 96.5 11 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
24d1biaa1



not modelled 96.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
25d1bw6a_



not modelled 96.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
26c2w48D_



not modelled 96.3 20 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
27d1j5ya1



not modelled 96.3 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
28d6paxa2



not modelled 96.1 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
29d1k78a2



not modelled 96.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
30c2vz4A_



not modelled 96.1 17 PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional activator tipa;
PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna
31c1r22B_



not modelled 96.1 14 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
32d1etob_



not modelled 96.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
33d1xsva_



not modelled 96.0 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
34c2zhhA_



not modelled 96.0 10 PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr
35d1r1ua_



not modelled 95.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
36c3mzyA_



not modelled 95.9 8 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
37d2ao9a1



not modelled 95.9 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
38d1b9ma1



not modelled 95.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:N-terminal domain of molybdate-dependent transcriptional regulator ModE
39d1q06a_



not modelled 95.8 20 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
40c3sztB_



not modelled 95.7 8 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
41c2cg4B_



not modelled 95.7 27 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
42c2q0oA_



not modelled 95.7 15 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
43d1r8da_



not modelled 95.7 19 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
44d1s7oa_



not modelled 95.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
45d1r1ta_



not modelled 95.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
46d1a04a1



not modelled 95.7 10 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)
47d1g2ha_



not modelled 95.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
48c1or7A_



not modelled 95.6 10 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
49c1x3uA_



not modelled 95.6 12 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
50c3f6oB_



not modelled 95.6 13 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
51c1zljE_



not modelled 95.5 18 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
52c3gpvA_



not modelled 95.5 9 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
53c1h0mD_



not modelled 95.5 11 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
54c3hugA_



not modelled 95.5 10 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
55c3hh0C_



not modelled 95.5 7 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
56d2bjca1



not modelled 95.4 23 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
57d1ulya_



not modelled 95.4 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein PH1932
58d1or7a1



not modelled 95.4 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
59d1fsea_



not modelled 95.4 9 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)
60d2d1ha1



not modelled 95.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
61d1rp3a2



not modelled 95.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
62c3r0aB_



not modelled 95.4 10 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
63c2vbzA_



not modelled 95.3 18 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
64c2krfB_



not modelled 95.3 7 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
65d1uxca_



not modelled 95.3 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
66c3qp5C_



not modelled 95.3 8 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
67c3jthA_



not modelled 95.3 12 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
68c3frwF_



not modelled 95.3 13 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
69c3m1eA_



not modelled 95.2 11 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator benm;
PDBTitle: crystal structure of benm_dbd
70d2esna1



not modelled 95.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LysR-like transcriptional regulators
71c2fxaB_



not modelled 95.2 12 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
72c2ijlB_



not modelled 95.2 11 PDB header:transcription
Chain: B: PDB Molecule:molybdenum-binding transcriptional repressor;
PDBTitle: the structure of a putative mode from agrobacterium tumefaciens.
73d1yioa1



not modelled 95.2 15 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)
74c2jpcA_



not modelled 95.2 18 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
75c1b9nA_



not modelled 95.2 15 PDB header:transcription
Chain: A: PDB Molecule:protein (mode);
PDBTitle: regulator from escherichia coli
76c1r71B_



not modelled 95.2 10 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
77c2o8xA_



not modelled 95.1 13 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
78c2l0kA_



not modelled 95.1 27 PDB header:transcription
Chain: A: PDB Molecule:stage iii sporulation protein d;
PDBTitle: nmr solution structure of a transcription factor spoiiid in complex2 with dna
79d1p4wa_



not modelled 95.1 19 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)
80c3f6vA_



not modelled 95.1 12 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
81c3gp4B_



not modelled 95.0 20 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes
82d1qpza1



not modelled 95.0 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
83c3qaoA_



not modelled 95.0 14 PDB header:transcription regulator
Chain: A: PDB Molecule:merr-like transcriptional regulator;
PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e
84c3cuoB_



not modelled 95.0 11 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
85c2jmlA_



not modelled 94.9 12 PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor
86c3korD_



not modelled 94.9 15 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
87c1bdhA_



not modelled 94.9 20 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
88d2hsga1



not modelled 94.9 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
89c1j5yA_



not modelled 94.9 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
90d2ezla_



not modelled 94.9 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
91c3fzjC_



not modelled 94.9 14 PDB header:transcription regulator
Chain: C: PDB Molecule:lysr type regulator of tsambcd;
PDBTitle: tsar low resolution crystal structure, tetragonal form
92d2p4wa1



not modelled 94.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
93d1l3la1



not modelled 94.9 10 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)
94d1ub9a_



not modelled 94.8 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
95c2jscB_



not modelled 94.8 9 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050;
PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
96d2p5ka1



not modelled 94.6 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
97c3pqkD_



not modelled 94.6 17 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
98d1uxda_



not modelled 94.5 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
99d1b4aa1



not modelled 94.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
100c1rp3G_



not modelled 94.5 15 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
101d1lnwa_



not modelled 94.5 4 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
102c2ia0A_



not modelled 94.5 14 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)
103d1mkma1



not modelled 94.5 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
104c2cfxD_



not modelled 94.5 8 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
105c2p6tH_



not modelled 94.5 13 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
106d1r8ea1



not modelled 94.4 9 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
107d1f9na1



not modelled 94.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
108c2e7xA_



not modelled 94.4 10 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
109d2isya1



not modelled 94.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
110c1iz1B_



not modelled 94.4 20 PDB header:dna binding protein
Chain: B: PDB Molecule:lysr-type regulatory protein;
PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator
111c2x4hA_



not modelled 94.3 5 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
112d1vz0a1



not modelled 94.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
113c2h09A_



not modelled 94.3 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
114d1lcda_



not modelled 94.3 22 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
115c3cloC_



not modelled 94.2 15 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
116c2zkzC_



not modelled 94.2 11 PDB header:transcription
Chain: C: PDB Molecule:transcriptional repressor pagr;
PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
117c2lcvA_



not modelled 94.2 20 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
118c2l4aA_



not modelled 94.2 12 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
119c3i4pA_



not modelled 94.2 24 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
120c2kkoB_



not modelled 94.1 12 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.

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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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