Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0CF64
DateThu Jan 5 11:31:22 GMT 2012
Unique Job IDec1d332d9030e7e6

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.
289 residues ( 94%) 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  MWTGKKVDSARALIARGWGVSLVSRCLRVSRAQLHVILRRTDDWMDGRRSRHTDDTDVLL
Secondary structure 

























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Disorder  ???











?























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





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
































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Disorder 


























?
























???????
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   .........130.........140.........150.........160.........170.........180
Sequence  AHTGRVAVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDREALHWAVTTGGFNSETVQD
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Disorder  ???

??




















































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   .........190.........200.........210.........220.........230.........240
Sequence  VMLGAVERRFGNDLPSSPVEWLTDNGSCYRANETRQFARMLGLEPKNTAVRSPESNGIAE
Secondary structure 






















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Disorder 









??















































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   .........250.........260.........270.........280.........290.........300
Sequence  SFVKTIKRDYISIMPKPDGLTAAKNLAEAFEHYNEWHPHSALGYRSPREYLRQRACNGLS
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Disorder 






















































?????
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   .......
Sequence  DNRCLEI
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: 128 - 296
Aligned: 152
Modelled: 169
Confidence: 99.9%
Identity: 18%
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: 122 - 287
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: 125 - 289
Aligned: 154
Modelled: 165
Confidence: 99.8%
Identity: 18%
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: 124 - 289
Aligned: 155
Modelled: 166
Confidence: 99.8%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1bco chain A domain 2

3D model

Region: 130 - 299
Aligned: 170
Modelled: 170
Confidence: 99.8%
Identity: 14%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 131 - 292
Aligned: 145
Modelled: 162
Confidence: 99.8%
Identity: 17%
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: 129 - 296
Aligned: 143
Modelled: 168
Confidence: 99.8%
Identity: 14%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1ex4 chain A

3D model

Region: 129 - 291
Aligned: 142
Modelled: 163
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: 133 - 294
Aligned: 144
Modelled: 160
Confidence: 99.7%
Identity: 17%
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: 130 - 275
Aligned: 133
Modelled: 146
Confidence: 99.7%
Identity: 19%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1bco chain A

3D model

Region: 127 - 299
Aligned: 172
Modelled: 173
Confidence: 99.7%
Identity: 13%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 1hyv chain A

3D model

Region: 131 - 293
Aligned: 134
Modelled: 163
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: 127 - 291
Aligned: 139
Modelled: 165
Confidence: 99.6%
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: 130 - 291
Aligned: 144
Modelled: 162
Confidence: 99.6%
Identity: 21%
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 1c6v chain A

3D model

Region: 134 - 294
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 3l2t chain B

3D model

Region: 128 - 299
Aligned: 160
Modelled: 163
Confidence: 99.6%
Identity: 15%
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 3hos chain A

3D model

Region: 8 - 274
Aligned: 256
Modelled: 267
Confidence: 99.5%
Identity: 14%
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: 129 - 291
Aligned: 141
Modelled: 154
Confidence: 99.3%
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: 2 - 111
Aligned: 110
Modelled: 110
Confidence: 98.8%
Identity: 17%
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: 2 - 102
Aligned: 101
Modelled: 101
Confidence: 98.8%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 2elh chain A

3D model

Region: 1 - 39
Aligned: 39
Modelled: 39
Confidence: 96.1%
Identity: 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

Phyre2
1

c3f9kV_
2

d1asua_
3

c1c0mA_
4

d1c0ma2
5

d1bcoa2
6

c3nf9A_
7

d1exqa_
8

c1ex4A_
9

c3kksB_
10

d1cxqa_
11

c1bcoA_
12

d1hyva_
13

c1k6yB_
14

c3hpgC_
15

d1c6va_
16

c3l2tB_
17

c3hosA_
18

c3dlrA_
19

c6paxA_
20

d1pdnc_
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c2elhA_
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Detailed template information 

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



99.9 18 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 18 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
5d1bcoa2



99.8 14 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
6c3nf9A_



99.8 17 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
7d1exqa_



99.8 14 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic 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 17 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 19 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
11c1bcoA_



99.7 13 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
12d1hyva_



99.7 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
13c1k6yB_



99.6 18 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
14c3hpgC_



99.6 21 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
15d1c6va_



99.6 19 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
16c3l2tB_



99.6 15 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)
17c3hosA_



99.5 14 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_



99.3 14 PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
19c6paxA_



98.8 17 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_



98.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
21c1u78A_



not modelled 98.6 10 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 98.4 18 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 98.0 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 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
25c3f2kB_



not modelled 97.2 20 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
26c3hefB_



not modelled 97.0 14 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
27d2coba1



not modelled 96.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
28d1k78a1



not modelled 96.8 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
29c1hlvA_



not modelled 96.7 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
30d6paxa1



not modelled 96.7 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
31c2rn7A_



not modelled 96.6 12 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
32c1umqA_



not modelled 96.4 24 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
33d1umqa_



not modelled 96.4 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
34d1ntca_



not modelled 96.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
35c2elhA_



96.1 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
36d1fipa_



not modelled 96.0 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
37d1etxa_



not modelled 95.9 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
38c3e7lD_



not modelled 95.8 8 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
39d1ijwc_



not modelled 95.6 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
40d1g2ha_



not modelled 95.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
41d1hcra_



not modelled 95.5 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
42d1etob_



not modelled 95.3 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
43d1a04a1



not modelled 94.7 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)
44d2ao9a1



not modelled 94.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
45c2w48D_



not modelled 94.5 14 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
46c3fmyA_



not modelled 94.5 6 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)
47c2cg4B_



not modelled 94.2 15 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
48c2jvlA_



not modelled 94.0 12 PDB header:transcription
Chain: A: PDB Molecule:trmbf1;
PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
49c1zljE_



not modelled 93.9 11 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
50d1fsea_



not modelled 93.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
51d1xsva_



not modelled 93.9 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
52d1hlva1



not modelled 93.7 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
53c2q0oA_



not modelled 93.6 8 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
54c3sztB_



not modelled 93.4 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
55d1s7oa_



not modelled 93.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
56c1r71B_



not modelled 93.4 13 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
57d1yioa1



not modelled 93.3 18 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)
58d2cg4a1



not modelled 93.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
59d1sq8a_



not modelled 93.1 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
60c3t76A_



not modelled 93.1 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator vanug;
PDBTitle: crystal structure of transcriptional regulator vanug, form ii
61d1l3la1



not modelled 92.8 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)
62d1bw6a_



not modelled 92.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
63c2krfB_



not modelled 92.7 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
64c3hugA_



not modelled 92.6 13 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
65c2l0kA_



not modelled 92.6 10 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
66d1r71a_



not modelled 92.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
67d1r69a_



not modelled 92.4 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
68d1biaa1



not modelled 92.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
69c1h0mD_



not modelled 92.3 22 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
70d1vz0a1



not modelled 92.1 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
71c1x3uA_



not modelled 92.1 11 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
72c2x48B_



not modelled 92.0 28 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
73d1p4wa_



not modelled 91.8 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)
74c3b7hA_



not modelled 91.8 3 PDB header:structural protein
Chain: A: PDB Molecule:prophage lp1 protein 11;
PDBTitle: crystal structure of the prophage lp1 protein 11
75c2xcjB_



not modelled 91.6 12 PDB header:viral protein
Chain: B: PDB Molecule:c protein;
PDBTitle: crystal structure of p2 c, the immunity repressor of2 temperate e. coli phage p2
76d1y9qa1



not modelled 91.6 26 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
77d1adra_



not modelled 91.6 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
78c3mzyA_



not modelled 91.6 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
79c2ia0A_



not modelled 91.6 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864;
PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864)
80c2iu5A_



not modelled 91.5 16 PDB header:transcription
Chain: A: PDB Molecule:hth-type dhaklm operon transcriptional activator dhas;
PDBTitle: dihydroxyacetone kinase operon activator dhas
81c3cecA_



not modelled 91.5 18 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
82c3qp5C_



not modelled 91.4 11 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
83c3o60A_



not modelled 91.4 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin0861 protein;
PDBTitle: the crystal structure of lin0861 from listeria innocua to 2.8a
84d1j5ya1



not modelled 91.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
85c2vbzA_



not modelled 91.4 24 PDB header:dna-binding protein
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan
86d2ezla_



not modelled 91.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
87c1z4hA_



not modelled 91.3 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
88c2rnjA_



not modelled 91.3 13 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
89c2w7nA_



not modelled 91.3 10 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
90c2ao9H_



not modelled 91.2 19 PDB header:structural genomics, unknown function
Chain: H: PDB Molecule:phage protein;
PDBTitle: structural genomics, the crystal structure of a phage protein2 (phbc6a51) from bacillus cereus atcc 14579
91d1rp3a2



not modelled 91.2 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
92c3op9A_



not modelled 91.2 9 PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua
93c2jpcA_



not modelled 91.0 17 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
94c3gn5B_



not modelled 90.8 6 PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
95d1nera_



not modelled 90.8 25 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
96c2p6tH_



not modelled 90.7 15 PDB header:transcription
Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family;
PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis
97c3c3wB_



not modelled 90.6 8 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
98c3ivpD_



not modelled 90.5 22 PDB header:dna binding protein
Chain: D: PDB Molecule:putative transposon-related dna-binding protein;
PDBTitle: the structure of a possible transposon-related dna-binding protein2 from clostridium difficile 630.
99d1or7a1



not modelled 90.3 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
100d2icta1



not modelled 90.3 12 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
101d1gdta1



not modelled 90.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
102c3onqB_



not modelled 90.2 10 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
103c2e7xA_



not modelled 90.2 12 PDB header:transcription regulator
Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator;
PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand
104c2np5A_



not modelled 90.2 17 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator (rha1_ro04179) from2 rhodococcus sp. rha1.
105c3f1bA_



not modelled 90.2 15 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.
106c2fjrB_



not modelled 90.1 11 PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186
107d1utxa_



not modelled 90.0 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
108d1uxca_



not modelled 90.0 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
109c1rnlA_



not modelled 90.0 19 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
110c1b0nA_



not modelled 90.0 20 PDB header:transcription regulator
Chain: A: PDB Molecule:protein (sinr protein);
PDBTitle: sinr protein/sini protein complex
111c2d6yA_



not modelled 89.9 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)
112c3gziA_



not modelled 89.9 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
113d2fq4a1



not modelled 89.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
114c2hxiA_



not modelled 89.8 25 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator from streptomyces coelicolor a3(2)
115c3eusB_



not modelled 89.7 14 PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding protein;
PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
116d2np5a1



not modelled 89.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
117c1bdhA_



not modelled 89.7 16 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
118d1lmb3_



not modelled 89.6 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
119c2e1cA_



not modelled 89.6 15 PDB header:transcription/dna
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519;
PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
120c2oqgA_



not modelled 89.6 21 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1

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