Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0CF53
DateThu Jan 5 11:31:07 GMT 2012
Unique Job ID28907f0c6fbcba1d

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3f9kV_
Top template information
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
Confidence and coverage
Confidence: 99.9% Coverage: 50%
152 residues ( 50% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
280 residues ( 93%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MDSARALIARGWGVSLVSRCLRVSRAQLHVILRRTDDWMDGRRSRHTDDTDVLLRIHHVI
Secondary structure 























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Disorder  ?







?























??????????????











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   .........70.........80.........90.........100.........110.........120
Sequence  GELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLERKPAVPPSKRAHTGRV
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Disorder 




















?
























??????????

?
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   .........130.........140.........150.........160.........170.........180
Sequence  AVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDREALHWAVTTGGFNSETVQDVMLGAV
Secondary structure 




















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   .........190.........200.........210.........220.........230.........240
Sequence  ERRFGNDLPSSPVEWLTDNGSCYRANETRQFARMLGLEPKNTAVRSPESNGIAESFVKTI
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Disorder 



??





















































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   .........250.........260.........270.........280.........290.........300
Sequence  KRDYISIMPKPDGLTAAKNLAEAFEHYNEWHPHSALGYRSPREYLRQRACNGLSDNRCLE
Secondary structure 
























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???????????
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   .
Sequence  I
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 3f9k chain V

3D model

Region: 122 - 290
Aligned: 152
Modelled: 169
Confidence: 99.9%
Identity: 17%
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd

Phyre2

PDB 1asu chain A

3D model

Region: 116 - 281
Aligned: 155
Modelled: 166
Confidence: 99.8%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1c0m chain A

3D model

Region: 118 - 283
Aligned: 155
Modelled: 166
Confidence: 99.8%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2

PDB 1c0m chain A domain 2

3D model

Region: 118 - 285
Aligned: 157
Modelled: 168
Confidence: 99.8%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 125 - 286
Aligned: 144
Modelled: 162
Confidence: 99.8%
Identity: 16%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design

Phyre2

PDB 1exq chain A

3D model

Region: 123 - 290
Aligned: 143
Modelled: 168
Confidence: 99.8%
Identity: 13%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1bco chain A domain 2

3D model

Region: 121 - 287
Aligned: 167
Modelled: 167
Confidence: 99.8%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2

PDB 1ex4 chain A

3D model

Region: 123 - 291
Aligned: 148
Modelled: 169
Confidence: 99.8%
Identity: 18%
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain

Phyre2

PDB 3kks chain B

3D model

Region: 127 - 290
Aligned: 146
Modelled: 164
Confidence: 99.7%
Identity: 16%
PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii

Phyre2

PDB 1cxq chain A

3D model

Region: 124 - 269
Aligned: 133
Modelled: 146
Confidence: 99.7%
Identity: 20%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1hyv chain A

3D model

Region: 128 - 287
Aligned: 131
Modelled: 160
Confidence: 99.7%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1k6y chain B

3D model

Region: 121 - 285
Aligned: 139
Modelled: 165
Confidence: 99.7%
Identity: 18%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2

PDB 3hpg chain C

3D model

Region: 121 - 289
Aligned: 151
Modelled: 169
Confidence: 99.6%
Identity: 20%
PDB header:transferase
Chain: C: PDB Molecule:integrase;
PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces

Phyre2

PDB 1bco chain A

3D model

Region: 121 - 292
Aligned: 171
Modelled: 172
Confidence: 99.6%
Identity: 14%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 3l2t chain B

3D model

Region: 121 - 291
Aligned: 159
Modelled: 171
Confidence: 99.6%
Identity: 14%
PDB header:recombination/dna
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)

Phyre2

PDB 1c6v chain A

3D model

Region: 128 - 288
Aligned: 133
Modelled: 148
Confidence: 99.6%
Identity: 19%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3hos chain A

3D model

Region: 3 - 292
Aligned: 277
Modelled: 290
Confidence: 99.6%
Identity: 13%
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 3dlr chain A

3D model

Region: 123 - 291
Aligned: 147
Modelled: 169
Confidence: 99.4%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase

Phyre2

PDB 6pax chain A

3D model

Region: 6 - 105
Aligned: 100
Modelled: 100
Confidence: 99.0%
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 1pdn chain C

3D model

Region: 6 - 96
Aligned: 91
Modelled: 91
Confidence: 98.9%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
1

c3f9kV_
2

d1asua_
3

c1c0mA_
4

d1c0ma2
5

c3nf9A_
6

d1exqa_
7

d1bcoa2
8

c1ex4A_
9

c3kksB_
10

d1cxqa_
11

d1hyva_
12

c1k6yB_
13

c3hpgC_
14

c1bcoA_
15

c3l2tB_
16

d1c6va_
17

c3hosA_
18

c3dlrA_
19

c6paxA_
20

d1pdnc_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3f9kV_



99.9 17 PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
2d1asua_



99.8 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
3c1c0mA_



99.8 17 PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
4d1c0ma2



99.8 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
5c3nf9A_



99.8 16 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
6d1exqa_



99.8 13 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
7d1bcoa2



99.8 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
8c1ex4A_



99.8 18 PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
9c3kksB_



99.7 16 PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii
10d1cxqa_



99.7 20 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
11d1hyva_



99.7 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
12c1k6yB_



99.7 18 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
13c3hpgC_



99.6 20 PDB header:transferase
Chain: C: PDB Molecule:integrase;
PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces
14c1bcoA_



99.6 14 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
15c3l2tB_



99.6 14 PDB header:recombination/dna
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)
16d1c6va_



99.6 19 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
17c3hosA_



99.6 13 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
18c3dlrA_



99.4 14 PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
19c6paxA_



99.0 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
20d1pdnc_



98.9 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
21c1u78A_



not modelled 98.6 11 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
22c2k27A_



not modelled 98.6 20 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
23c2f7tA_



not modelled 97.8 14 PDB header:dna binding protein
Chain: A: PDB Molecule:mos1 transposase;
PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase
24d2jn6a1



not modelled 97.8 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
25c3f2kB_



not modelled 97.4 18 PDB header:transferase
Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar;
PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar
26d1k78a1



not modelled 96.8 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
27d6paxa1



not modelled 96.6 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
28c2rn7A_



not modelled 96.6 13 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
29c1hlvA_



not modelled 96.3 11 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
30c1umqA_



not modelled 96.2 27 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
31d1umqa_



not modelled 96.2 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
32c2w48D_



not modelled 96.1 13 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
33d1ntca_



not modelled 96.0 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
34c3hefB_



not modelled 95.9 17 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
35d1fipa_



not modelled 95.8 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
36d1etxa_



not modelled 95.8 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
37c3e7lD_



not modelled 95.4 6 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
38c2elhA_



not modelled 95.3 21 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
39d1etob_



not modelled 95.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
40d1g2ha_



not modelled 94.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
41d2coba1



not modelled 94.6 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
42c2x48B_



not modelled 94.2 26 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
43c3bs3A_



not modelled 94.0 9 PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna-binding protein;
PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis
44c2w7nA_



not modelled 93.2 11 PDB header:transcription/dna
Chain: A: PDB Molecule:trfb transcriptional repressor protein;
PDBTitle: crystal structure of kora bound to operator dna: insight2 into repressor cooperation in rp4 gene regulation
45d1hlva1



not modelled 93.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
46c1r71B_



not modelled 93.0 16 PDB header:transcription/dna
Chain: B: PDB Molecule:transcriptional repressor protein korb;
PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna
47d1r71a_



not modelled 92.5 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
48c3onqB_



not modelled 92.5 15 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:regulator of polyketide synthase expression;
PDBTitle: crystal structure of regulator of polyketide synthase expression2 bad_0249 from bifidobacterium adolescentis
49c1bdhA_



not modelled 92.3 16 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
50c1z4hA_



not modelled 92.3 4 PDB header:protein binding, dna binding protein
Chain: A: PDB Molecule:tor inhibition protein;
PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase
51d1a04a1



not modelled 92.3 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
52d1ijwc_



not modelled 92.2 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
53d1rzsa_



not modelled 92.2 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
54d1hcra_



not modelled 92.2 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
55c3t76A_



not modelled 92.1 17 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator vanug;
PDBTitle: crystal structure of transcriptional regulator vanug, form ii
56d1vz0a1



not modelled 92.1 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
57c3b7hA_



not modelled 92.0 3 PDB header:structural protein
Chain: A: PDB Molecule:prophage lp1 protein 11;
PDBTitle: crystal structure of the prophage lp1 protein 11
58c3cecA_



not modelled 92.0 10 PDB header:transcription
Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system;
PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
59c2d6yA_



not modelled 92.0 19 PDB header:gene regulation
Chain: A: PDB Molecule:putative tetr family regulatory protein;
PDBTitle: crystal structure of transcriptional factor sco4008 from streptomyces2 coelicolor a3(2)
60c3h5tA_



not modelled 91.8 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
61c2kpjA_



not modelled 91.8 8 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
62c3f1bA_



not modelled 91.7 16 PDB header:transcription regulator
Chain: A: PDB Molecule:tetr-like transcriptional regulator;
PDBTitle: the crystal structure of a tetr-like transcriptional regulator from2 rhodococcus sp. rha1.
63d1t56a1



not modelled 91.7 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
64c3omtA_



not modelled 91.7 8 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
65d1gdta1



not modelled 91.7 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
66c3gziA_



not modelled 91.7 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of a transcriptional regulator of the tetr family2 (shew_3567) from shewanella loihica pv-4 at 2.05 a resolution
67c2l0kA_



not modelled 91.6 13 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
68c1vi0B_



not modelled 91.5 23 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator
69c1ui6B_



not modelled 91.5 23 PDB header:antibiotic
Chain: B: PDB Molecule:a-factor receptor homolog;
PDBTitle: crystal structure of gamma-butyrolactone receptor (arpa-like protein)
70d2fq4a1



not modelled 91.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
71d1bw6a_



not modelled 91.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
72c1zljE_



not modelled 91.3 10 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
73c3bjbE_



not modelled 91.3 16 PDB header:transcription regulator
Chain: E: PDB Molecule:probable transcriptional regulator, tetr family protein;
PDBTitle: crystal structure of a tetr transcriptional regulator from rhodococcus2 sp. rha1
74d1yioa1



not modelled 91.2 17 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)
75c2of7A_



not modelled 91.1 16 PDB header:transcription
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: structural genomics, the crystal structure of a tetr-family2 transcriptional regulator from streptomyces coelicolor a3
76c2guhA_



not modelled 91.1 23 PDB header:transcription
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of the putative tetr-family transcriptional2 regulator from rhodococcus sp. rha1
77c1jumB_



not modelled 91.1 13 PDB header:transcription
Chain: B: PDB Molecule:hypothetical transcriptional regulator in qaca
PDBTitle: crystal structure of the multidrug binding transcriptional2 repressor qacr bound to the natural drug berberine
78c2nx4A_



not modelled 91.1 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:transcriptional regulator, tetr family protein;
PDBTitle: the crystal structure of athe putative tetr-family transcriptional2 regulator rha06780 from rhodococcus sp. rha1.
79c1bjzA_



not modelled 91.1 19 PDB header:transcription regulation
Chain: A: PDB Molecule:tetracycline repressor;
PDBTitle: tetracycline chelated mg2+-ion initiates helix unwinding for tet2 repressor induction
80d2bjca1



not modelled 91.1 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
81c3mzyA_



not modelled 91.0 13 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
82c3bcgA_



not modelled 91.0 16 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator acrr;
PDBTitle: conformational changes of the acrr regulator reveal a2 mechanism of induction
83d1jt6a1



not modelled 91.0 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
84c2genA_



not modelled 90.9 13 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional regulator;
PDBTitle: structural genomics, the crystal structure of a probable2 transcriptional regulator from pseudomonas aeruginosa pao1
85c2krfB_



not modelled 90.9 14 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
86c1zvvA_



not modelled 90.8 18 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
87c3cjdB_



not modelled 90.7 16 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of putative tetr transcriptional regulator2 (yp_510936.1) from jannaschia sp. ccs1 at 1.79 a resolution
88c3b6aC_



not modelled 90.7 13 PDB header:transcription
Chain: C: PDB Molecule:actr protein;
PDBTitle: crystal structure of the streptomyces coelicolor tetr2 family protein actr in complex with actinorhodin
89c2rasB_



not modelled 90.7 29 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of a putative tetr/acrr family transcriptional2 regulator (saro_0558) from novosphingobium aromaticivorans dsm at3 1.80 a resolution
90c1x3uA_



not modelled 90.7 14 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
91d1uxca_



not modelled 90.6 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
92c3ppbB_



not modelled 90.6 19 PDB header:transcription regulator
Chain: B: PDB Molecule:putative tetr family transcription regulator;
PDBTitle: crystal structure of a putative tetr family transcription regulator2 (shew_3104) from shewanella sp. pv-4 at 2.10 a resolution
93c2gfnA_



not modelled 90.6 29 PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional regulator pksa related protein;
PDBTitle: crystal structure of hth-type transcriptional regulator pksa related2 protein from rhodococcus sp. rha1
94c2zcxA_



not modelled 90.6 23 PDB header:transcription
Chain: A: PDB Molecule:tetr-family transcriptional regulator;
PDBTitle: crystal structure of tetr family transcriptional regulator2 sco7815
95d2hsga1



not modelled 90.6 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
96d1nera_



not modelled 90.5 26 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
97c2zb9A_



not modelled 90.5 19 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of tetr family transcription regulator2 sco0332
98d1lcda_



not modelled 90.5 12 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
99d1p4wa_



not modelled 90.5 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)
100c2wuiA_



not modelled 90.4 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of mexz, a key repressor responsible for2 antibiotic resistance in pseudomonas aeruginosa.
101c2hytA_



not modelled 90.4 16 PDB header:transcription
Chain: A: PDB Molecule:tetr-family transcriptional regulator;
PDBTitle: crystal structure of a tetr-family transcriptional regulator (eca1819)2 from pectobacterium atrosepticum at 1.64 a resolution
102c2f07A_



not modelled 90.4 10 PDB header:transcription
Chain: A: PDB Molecule:yvdt;
PDBTitle: crystal structure of yvdt from bacillus subtilis
103d1utxa_



not modelled 90.4 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
104c3dewA_



not modelled 90.4 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: the structure of a putative tetr family transcriptional regulator from2 geobacter sulfurreducens pca.
105c3anpD_



not modelled 90.4 19 PDB header:transcription
Chain: D: PDB Molecule:transcriptional repressor, tetr family;
PDBTitle: crystal structure of thermus thermophilus fadr, a tetr familly2 transcriptional repressor, in complex with lauroyl-coa.
106c2fq4A_



not modelled 90.4 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: the crystal structure of the transcriptional regulator (tetr family)2 from bacillus cereus
107c3on4D_



not modelled 90.4 19 PDB header:transcription
Chain: D: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of tetr transcriptional regulator from legionella2 pneumophila
108c2dg7A_



not modelled 90.4 13 PDB header:gene regulation
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator sco03372 from streptomyces coelicolor a3(2)
109c2cg4B_



not modelled 90.3 19 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
110c3c2bA_



not modelled 90.3 23 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of tetr transcriptional regulator from agrobacterium2 tumefaciens
111c2qtqB_



not modelled 90.3 13 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of a predicted dna-binding transcriptional regulator2 (saro_1072) from novosphingobium aromaticivorans dsm at 1.85 a3 resolution
112d3c07a1



not modelled 90.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
113c3c07B_



not modelled 90.3 16 PDB header:transcription regulator
Chain: B: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of a tetr family transcriptional regulator from2 streptomyces coelicolor a3(2)
114c3b81A_



not modelled 90.3 10 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, acrr family;
PDBTitle: crystal structure of predicted dna-binding transcriptional regulator2 of tetr/acrr family (np_350189.1) from clostridium acetobutylicum at3 2.10 a resolution
115c2o7tA_



not modelled 90.3 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a tetr family transcriptional regulator2 (ncgl1578, cgl1640) from corynebacterium glutamicum at 2.10 a3 resolution
116c3dcfB_



not modelled 90.2 6 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator of the tetr/acrr
PDBTitle: crystal structure of transcriptional regulator of the2 tetr/acrr family (yp_290855.1) from thermobifida fusca yx-3 er1 at 2.50 a resolution
117c3fiwB_



not modelled 90.2 19 PDB header:transcription regulator
Chain: B: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: structure of sco0253, a tetr-family transcriptional regulator from2 streptomyces coelicolor
118d1ui5a1



not modelled 90.1 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
119c2jpcA_



not modelled 90.1 21 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
120c3fmyA_



not modelled 90.1 3 PDB header:dna binding protein
Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa
PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021)

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