Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77170
DateWed Jan 25 15:21:10 GMT 2012
Unique Job ID6af8b01e529ff1fa

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2gm4B_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage: 90%
177 residues ( 90% 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  MSQIFAYCRISTLDQTTENQRREIESAGFKIKPQQIIEEHISGSAATSERPGFNRLLARL
Secondary structure 























SS confidence 



























































Disorder  ??









































??????









Disorder confidence 



























































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

















SS confidence 



























































Disorder 










































??














Disorder confidence 



























































 
   .........130.........140.........150.........160.........170.........180
Sequence  AEFERDLLLERTHSGIVRARGAGKRFGRPPVLNEEQKQAVFERIKSGVSISAIAREFKTS
Secondary structure 


















SS confidence 



























































Disorder 





















????
?































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   .........190......
Sequence  RQTILRAKAKLQTPDI
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 2gm4 chain B

3D model

Region: 4 - 192
Aligned: 177
Modelled: 189
Confidence: 100.0%
Identity: 31%
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

Phyre2

PDB 2r0q chain F

3D model

Region: 4 - 191
Aligned: 176
Modelled: 188
Confidence: 100.0%
Identity: 28%
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 1gdt chain A domain 2

3D model

Region: 3 - 146
Aligned: 139
Modelled: 144
Confidence: 99.9%
Identity: 34%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 2gm4 chain A domain 2

3D model

Region: 1 - 146
Aligned: 136
Modelled: 145
Confidence: 99.9%
Identity: 35%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3g13 chain B

3D model

Region: 1 - 127
Aligned: 126
Modelled: 127
Confidence: 99.9%
Identity: 25%
PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile

Phyre2

PDB 3guv chain A

3D model

Region: 3 - 142
Aligned: 137
Modelled: 140
Confidence: 99.9%
Identity: 27%
PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein;
PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae

Phyre2

PDB 3lhk chain A

3D model

Region: 2 - 144
Aligned: 140
Modelled: 143
Confidence: 99.9%
Identity: 17%
PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna binding protein mj0014;
PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii.

Phyre2

PDB 3pkz chain K

3D model

Region: 4 - 124
Aligned: 116
Modelled: 121
Confidence: 99.9%
Identity: 25%
PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase

Phyre2

PDB 3bvp chain B

3D model

Region: 2 - 128
Aligned: 126
Modelled: 127
Confidence: 99.9%
Identity: 26%
PDB header:recombination
Chain: B: PDB Molecule:tp901-1 integrase;
PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase

Phyre2

PDB 3plo chain X

3D model

Region: 4 - 132
Aligned: 122
Modelled: 129
Confidence: 99.9%
Identity: 39%
PDB header:recombination
Chain: X: PDB Molecule:dna-invertase;
PDBTitle: crystal structure of the fis-independent mutant of gin

Phyre2

PDB 2rsl chain A

3D model

Region: 1 - 128
Aligned: 115
Modelled: 128
Confidence: 99.9%
Identity: 33%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3lhf chain C

3D model

Region: 2 - 141
Aligned: 129
Modelled: 140
Confidence: 99.8%
Identity: 20%
PDB header:recombination
Chain: C: PDB Molecule:serine recombinase;
PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a

Phyre2

PDB 1hx7 chain A

3D model

Region: 1 - 111
Aligned: 105
Modelled: 110
Confidence: 99.8%
Identity: 30%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 1pdn chain C

3D model

Region: 140 - 195
Aligned: 56
Modelled: 56
Confidence: 97.7%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 6pax chain A

3D model

Region: 140 - 195
Aligned: 56
Modelled: 56
Confidence: 97.7%
Identity: 18%
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 1u78 chain A

3D model

Region: 147 - 195
Aligned: 49
Modelled: 49
Confidence: 97.7%
Identity: 16%
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 1k78 chain A domain 1

3D model

Region: 143 - 193
Aligned: 51
Modelled: 51
Confidence: 97.5%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 6pax chain A domain 1

3D model

Region: 143 - 193
Aligned: 51
Modelled: 51
Confidence: 97.4%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 2k27 chain A

3D model

Region: 143 - 195
Aligned: 53
Modelled: 53
Confidence: 97.0%
Identity: 19%
PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain

Phyre2

PDB 2jn6 chain A domain 1

3D model

Region: 149 - 195
Aligned: 47
Modelled: 47
Confidence: 96.7%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Cgl2762-like

Phyre2
1

c2gm4B_
2

c2r0qF_
3

d1gdta2
4

d2gm4a2
5

c3g13B_
6

c3guvA_
7

c3lhkA_
8

c3pkzK_
9

c3bvpB_
10

c3ploX_
11

d2rsla_
12

c3lhfC_
13

d1hx7a_
14

d1pdnc_
15

c6paxA_
16

c1u78A_
17

d1k78a1
18

d6paxa1
19

c2k27A_
20

d2jn6a1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2gm4B_



100.0 31 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
2c2r0qF_



100.0 28 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
3d1gdta2



99.9 34 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
4d2gm4a2



99.9 35 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
5c3g13B_



99.9 25 PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile
6c3guvA_



99.9 27 PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein;
PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae
7c3lhkA_



99.9 17 PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna binding protein mj0014;
PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii.
8c3pkzK_



99.9 25 PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase
9c3bvpB_



99.9 26 PDB header:recombination
Chain: B: PDB Molecule:tp901-1 integrase;
PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase
10c3ploX_



99.9 39 PDB header:recombination
Chain: X: PDB Molecule:dna-invertase;
PDBTitle: crystal structure of the fis-independent mutant of gin
11d2rsla_



99.9 33 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
12c3lhfC_



99.8 20 PDB header:recombination
Chain: C: PDB Molecule:serine recombinase;
PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a
13d1hx7a_



99.8 30 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
14d1pdnc_



97.7 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
15c6paxA_



97.7 18 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
16c1u78A_



97.7 16 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
17d1k78a1



97.5 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
18d6paxa1



97.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
19c2k27A_



97.0 19 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
20d2jn6a1



96.7 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
21d1ijwc_



not modelled 96.6 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
22d1hcra_



not modelled 96.5 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
23c2krfB_



not modelled 96.2 11 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
24d1p4wa_



not modelled 96.2 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
25c2rn7A_



not modelled 96.1 16 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
26c1zljE_



not modelled 96.1 16 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
27c2l4aA_



not modelled 96.0 14 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
28c3hugA_



not modelled 96.0 22 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
29d1a04a1



not modelled 96.0 16 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)
30d1fsea_



not modelled 96.0 21 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)
31c1x3uA_



not modelled 95.9 22 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
32c3sztB_



not modelled 95.9 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
33d1yioa1



not modelled 95.8 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)
34c3mzyA_



not modelled 95.8 16 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
35c3hefB_



not modelled 95.8 21 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
36c1h0mD_



not modelled 95.8 6 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
37d1l3la1



not modelled 95.8 11 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)
38d1xsva_



not modelled 95.7 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
39c2q0oA_



not modelled 95.7 13 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
40c2jpcA_



not modelled 95.6 18 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
41c2rnjA_



not modelled 95.5 18 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
42d2isya1



not modelled 95.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
43c2oqgA_



not modelled 95.4 23 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
44c1r22B_



not modelled 95.4 9 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
45c3qp5C_



not modelled 95.3 19 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
46d1gdta1



not modelled 95.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
47d1or7a1



not modelled 95.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
48d2cg4a1



not modelled 95.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
49d1r1ta_



not modelled 95.2 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
50d2cfxa1



not modelled 95.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
51c3frwF_



not modelled 95.1 19 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
52c1f5tA_



not modelled 95.1 21 PDB header:transcription/dna
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
53d1biaa1



not modelled 95.1 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
54d2d1ha1



not modelled 95.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
55d2ev0a1



not modelled 95.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
56d1ulya_



not modelled 95.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein PH1932
57c3c3wB_



not modelled 95.1 16 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
58c2jscB_



not modelled 95.1 9 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050;
PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
59c2cfxD_



not modelled 95.0 21 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
60c2elhA_



not modelled 95.0 24 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
61d2cyya1



not modelled 95.0 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
62d1rp3a2



not modelled 95.0 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
63c3cloC_



not modelled 95.0 24 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
64d1r1ua_



not modelled 95.0 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
65c3korD_



not modelled 94.9 38 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
66c2o8xA_



not modelled 94.9 16 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
67c1or7A_



not modelled 94.9 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
68d1g3wa1



not modelled 94.9 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
69c2ev5B_



not modelled 94.8 17 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
70c2h09A_



not modelled 94.8 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
71d1s7oa_



not modelled 94.8 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
72c2it0A_



not modelled 94.7 14 PDB header:transcription/dna
Chain: A: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
73c3pqkD_



not modelled 94.7 12 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
74c3f6vA_



not modelled 94.7 21 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
75d1ttya_



not modelled 94.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
76c2x4hA_



not modelled 94.7 16 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
77c3tgnA_



not modelled 94.6 16 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
78d1i1ga1



not modelled 94.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
79c1rp3G_



not modelled 94.6 23 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
80d2coba1



not modelled 94.6 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
81c3f6oB_



not modelled 94.5 19 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
82d1j5ya1



not modelled 94.5 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
83c1rnlA_



not modelled 94.3 15 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
84c3by6C_



not modelled 94.2 15 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
85c2kkoB_



not modelled 94.1 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.
86d1sfxa_



not modelled 94.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
87c3cuoB_



not modelled 94.0 14 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
88d1ku3a_



not modelled 94.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
89c2wteB_



not modelled 93.9 19 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.
90c3jthA_



not modelled 93.9 12 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
91d1mkma1



not modelled 93.9 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
92d2p7vb1



not modelled 93.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
93c3hosA_



not modelled 93.8 12 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
94d1ku7a_



not modelled 93.8 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
95d1jhfa1



not modelled 93.8 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
96d1trra_



not modelled 93.7 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
97d1hlva1



not modelled 93.6 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
98c3klnC_



not modelled 93.6 12 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
99d1smyf2



not modelled 93.5 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
100c1r71B_



not modelled 93.4 23 PDB header:transcription/dna
Chain: B: PDB Molecule:transcriptional repressor protein korb;
PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna
101d1r71a_



not modelled 93.4 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
102d1jhga_



not modelled 93.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
103d1ub9a_



not modelled 93.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
104c3g3zA_



not modelled 93.0 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
105c3nqoB_



not modelled 92.9 26 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
106c2rdpA_



not modelled 92.9 9 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
107c3r0aB_



not modelled 92.8 18 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
108d2etha1



not modelled 92.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
109d2fxaa1



not modelled 92.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
110c2qwwB_



not modelled 92.6 11 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution
111c1hlvA_



not modelled 92.5 16 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:major centromere autoantigen b;
PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna
112d1stza1



not modelled 92.4 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
113c2fa5B_



not modelled 92.4 15 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
114d3bwga1



not modelled 92.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
115c2kpjA_



not modelled 92.3 23 PDB header:transcription regulator
Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa;
PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a
116c3f3xA_



not modelled 92.2 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
117c3neuA_



not modelled 92.2 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
118d1rr7a_



not modelled 92.1 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Middle operon regulator, Mor
119c1rr7A_



not modelled 92.1 12 PDB header:transcription
Chain: A: PDB Molecule:middle operon regulator;
PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu
120d1ku9a_



not modelled 92.0 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223

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