Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0ADI0
DateWed Jan 25 15:20:28 GMT 2012
Unique Job IDa8fcefe2b868a38e

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: 89%
175 residues ( 89% 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  MSRIFAYCRISTLDQTTENQRREIESAGFKIKPQQIIEEHISGSAATSERPGFNRLLARL
Secondary structure 























SS confidence 



























































Disorder  ??









































??????









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


















SS confidence 



























































Disorder 










































??














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   .........130.........140.........150.........160.........170.........180
Sequence  AEFERDLLLERTHSGIVRARGAGKRFGRPPVLNEEQKQVVFERIKSGVSISAIAREFKTS
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 - 190
Aligned: 175
Modelled: 187
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: 1 - 190
Aligned: 176
Modelled: 188
Confidence: 100.0%
Identity: 29%
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 - 145
Aligned: 138
Modelled: 143
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 - 145
Aligned: 135
Modelled: 144
Confidence: 99.9%
Identity: 35%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3guv chain A

3D model

Region: 3 - 142
Aligned: 137
Modelled: 140
Confidence: 99.9%
Identity: 29%
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 3g13 chain B

3D model

Region: 1 - 127
Aligned: 126
Modelled: 127
Confidence: 99.9%
Identity: 26%
PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile

Phyre2

PDB 3pkz chain K

3D model

Region: 1 - 124
Aligned: 117
Modelled: 122
Confidence: 99.9%
Identity: 29%
PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase

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 3plo chain X

3D model

Region: 4 - 132
Aligned: 122
Modelled: 129
Confidence: 99.8%
Identity: 42%
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: 99.8%
Identity: 34%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3bvp chain B

3D model

Region: 2 - 128
Aligned: 126
Modelled: 127
Confidence: 99.8%
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 3lhf chain C

3D model

Region: 2 - 141
Aligned: 129
Modelled: 138
Confidence: 99.8%
Identity: 22%
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 - 109
Aligned: 104
Modelled: 109
Confidence: 99.8%
Identity: 29%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 1pdn chain C

3D model

Region: 143 - 195
Aligned: 53
Modelled: 53
Confidence: 97.7%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 6pax chain A

3D model

Region: 143 - 195
Aligned: 53
Modelled: 53
Confidence: 97.7%
Identity: 19%
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: 148 - 195
Aligned: 48
Modelled: 48
Confidence: 97.6%
Identity: 17%
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: 97.3%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 2jn6 chain A domain 1

3D model

Region: 149 - 195
Aligned: 47
Modelled: 47
Confidence: 97.2%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Cgl2762-like

Phyre2

PDB 2k27 chain A

3D model

Region: 143 - 195
Aligned: 53
Modelled: 53
Confidence: 96.8%
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 1jhf chain A domain 1

3D model

Region: 169 - 195
Aligned: 27
Modelled: 27
Confidence: 93.1%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: LexA repressor, N-terminal DNA-binding domain

Phyre2
1

c2gm4B_
2

c2r0qF_
3

d1gdta2
4

d2gm4a2
5

c3guvA_
6

c3g13B_
7

c3pkzK_
8

c3lhkA_
9

c3ploX_
10

d2rsla_
11

c3bvpB_
12

c3lhfC_
13

d1hx7a_
14

d1pdnc_
15

c6paxA_
16

c1u78A_
17

d1k78a1
18

d6paxa1
19

d2jn6a1
20

c2k27A_
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d1jhfa1
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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 29 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
5c3guvA_



99.9 29 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
6c3g13B_



99.9 26 PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile
7c3pkzK_



99.9 29 PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase
8c3lhkA_



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.
9c3ploX_



99.8 42 PDB header:recombination
Chain: X: PDB Molecule:dna-invertase;
PDBTitle: crystal structure of the fis-independent mutant of gin
10d2rsla_



99.8 34 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
11c3bvpB_



99.8 26 PDB header:recombination
Chain: B: PDB Molecule:tp901-1 integrase;
PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase
12c3lhfC_



99.8 22 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 29 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
14d1pdnc_



97.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
15c6paxA_



97.7 19 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_



97.6 17 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



97.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
19d2jn6a1



97.2 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
20c2k27A_



96.8 19 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
21d1ijwc_



not modelled 96.6 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
22c2l4aA_



not modelled 96.6 17 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
23d1hcra_



not modelled 96.6 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
24c2rn7A_



not modelled 96.5 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
25c2krfB_



not modelled 96.4 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
26d1p4wa_



not modelled 96.3 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)
27c3frwF_



not modelled 96.3 21 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
28d1fsea_



not modelled 96.3 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)
29c1zljE_



not modelled 96.3 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
30d2cg4a1



not modelled 96.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
31c3korD_



not modelled 96.2 38 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
32c3hugA_



not modelled 96.2 19 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
33d1a04a1



not modelled 96.2 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)
34d1trra_



not modelled 96.2 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
35c3sztB_



not modelled 96.1 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
36d1yioa1



not modelled 96.1 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)
37d2cfxa1



not modelled 96.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
38c1x3uA_



not modelled 96.1 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
39c3hefB_



not modelled 96.0 21 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
40c3mzyA_



not modelled 96.0 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
41d1l3la1



not modelled 96.0 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)
42d1jhga_



not modelled 96.0 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
43c2cfxD_



not modelled 96.0 20 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
44d1xsva_



not modelled 96.0 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
45d2cyya1



not modelled 96.0 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
46c1h0mD_



not modelled 95.9 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
47c2q0oA_



not modelled 95.9 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
48c2jpcA_



not modelled 95.8 18 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
49c2rnjA_



not modelled 95.8 18 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
50d1rp3a2



not modelled 95.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
51c2oqgA_



not modelled 95.7 24 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
52d2isya1



not modelled 95.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
53d1or7a1



not modelled 95.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
54d1r1ta_



not modelled 95.6 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
55d1i1ga1



not modelled 95.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
56d1r1ua_



not modelled 95.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
57c3qp5C_



not modelled 95.4 21 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
58c1r22B_



not modelled 95.3 11 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
59d2d1ha1



not modelled 95.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
60c3cloC_



not modelled 95.3 21 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
61c2jscB_



not modelled 95.3 9 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050;
PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
62c1or7A_



not modelled 95.3 21 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
63c3c3wB_



not modelled 95.3 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
64c3pqkD_



not modelled 95.2 12 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
65d1biaa1



not modelled 95.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
66c3f6vA_



not modelled 95.2 21 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
67c2o8xA_



not modelled 95.2 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
68c2elhA_



not modelled 95.1 22 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
69d2ev0a1



not modelled 95.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
70c3f6oB_



not modelled 95.1 16 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
71d1g3wa1



not modelled 95.1 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
72c3tgnA_



not modelled 95.1 15 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
73d1s7oa_



not modelled 95.0 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
74d1ulya_



not modelled 95.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein PH1932
75d1mkma1



not modelled 95.0 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
76c2h09A_



not modelled 94.9 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
77c1rp3G_



not modelled 94.9 25 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
78c1f5tA_



not modelled 94.9 19 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
79d1j5ya1



not modelled 94.8 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
80c3klnC_



not modelled 94.8 16 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
81d1ttya_



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
82c2ev5B_



not modelled 94.6 18 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
83d1ub9a_



not modelled 94.6 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
84d1smyf2



not modelled 94.6 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
85c2x4hA_



not modelled 94.6 17 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
86c2kkoB_



not modelled 94.6 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.
87c1rnlA_



not modelled 94.5 16 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
88c3by6C_



not modelled 94.4 14 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
89c2it0A_



not modelled 94.4 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
90c2wteB_



not modelled 94.3 11 PDB header:antiviral protein
Chain: B: PDB Molecule:csa3;
PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
91c3cuoB_



not modelled 94.2 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
92d1gdta1



not modelled 94.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
93d1hlva1



not modelled 94.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
94c3jthA_



not modelled 94.1 16 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
95d2fxaa1



not modelled 94.0 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
96c1r71B_



not modelled 94.0 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
97d1sfxa_



not modelled 93.9 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
98d2etha1



not modelled 93.8 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
99d1ku3a_



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
100d1hw1a1



not modelled 93.7 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
101d1r71a_



not modelled 93.7 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
102c3neuA_



not modelled 93.7 17 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
103c3r0aB_



not modelled 93.7 20 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
104d2p7vb1



not modelled 93.7 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
105d2hs5a1



not modelled 93.5 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
106d1ku7a_



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
107d2coba1



not modelled 93.5 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
108c3g3zA_



not modelled 93.4 17 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
109c3nqoB_



not modelled 93.4 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
110c3f3xA_



not modelled 93.3 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
111c2rdpA_



not modelled 93.1 9 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
112d2hr3a1



not modelled 93.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
113d1u2wa1



not modelled 93.1 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
114d1jhfa1



93.1 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
115c1hlvA_



not modelled 93.0 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
116c2qwwB_



not modelled 92.9 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
117c3hosA_



not modelled 92.9 10 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
118d1lnwa_



not modelled 92.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
119d1ku9a_



not modelled 92.7 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
120c2fa5B_



not modelled 92.6 17 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

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