Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0CF88
DateThu Jan 5 11:31:46 GMT 2012
Unique Job ID02075b3a88d9a7ed

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1exqa_
Top template information
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
Confidence and coverage
Confidence: 99.9% Coverage: 37%
141 residues ( 37% 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.
332 residues ( 87%) 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  MRRTFTAEEKASVFELWKNGTGFSEIANILGSKPGTIFTMLRDTGGIKPHERKRAVAHLT
Secondary structure 




























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Disorder  ??????
























?













????????????
?
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   .........70.........80.........90.........100.........110.........120
Sequence  LSEREEIRAGLSAKMSIRAIATALNRSPSTISREVQRNRGRRYYKAVDANNRANRMAKRP
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?
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?
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   .........130.........140.........150.........160.........170.........180
Sequence  KPCLLDQNLPLRKLVLEKLEMKWSPEQISGWLRRTKPRQKTLRISPETIYKTLYFRSREA
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?


















?
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   .........190.........200.........210.........220.........230.........240
Sequence  LHHLNIQHLRRSHSLRHGRRHTRKGERGTINIVNGTPIHERSRNIDNRRSLGHWEGDLVS
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????????????????????
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   .........250.........260.........270.........280.........290.........300
Sequence  GTKNSHIATLVDRKSRYTIIVRLRGKDSVSVNQALTDKFLSLPSELRKSLTWDRGMELAR
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   .........310.........320.........330.........340.........350.........360
Sequence  HLEFTVSTGVKVYFCDPQSPWQRGTNENTNGLIRQYFPKKTCLAQYTQHELDLVAAQLNN
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???



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   .........370.........380...
Sequence  RPRKTLKFKTPKEIIERGVALTD
Secondary structure 










SS confidence 






















Disorder 




?












????
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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 1exq chain A

3D model

Region: 229 - 380
Aligned: 141
Modelled: 152
Confidence: 99.9%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3f9k chain V

3D model

Region: 224 - 375
Aligned: 148
Modelled: 152
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 1c6v chain A

3D model

Region: 229 - 381
Aligned: 138
Modelled: 153
Confidence: 99.9%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1hyv chain A

3D model

Region: 231 - 380
Aligned: 136
Modelled: 150
Confidence: 99.9%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1ex4 chain A

3D model

Region: 229 - 375
Aligned: 140
Modelled: 147
Confidence: 99.9%
Identity: 16%
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 231 - 379
Aligned: 145
Modelled: 149
Confidence: 99.9%
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 1c0m chain A domain 2

3D model

Region: 234 - 375
Aligned: 139
Modelled: 142
Confidence: 99.8%
Identity: 20%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3kks chain B

3D model

Region: 232 - 378
Aligned: 142
Modelled: 147
Confidence: 99.8%
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 1asu chain A

3D model

Region: 213 - 371
Aligned: 148
Modelled: 151
Confidence: 99.8%
Identity: 19%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3hpg chain C

3D model

Region: 231 - 375
Aligned: 140
Modelled: 145
Confidence: 99.8%
Identity: 18%
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 1c0m chain A

3D model

Region: 231 - 375
Aligned: 142
Modelled: 145
Confidence: 99.8%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2

PDB 1k6y chain B

3D model

Region: 231 - 380
Aligned: 137
Modelled: 150
Confidence: 99.8%
Identity: 15%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2

PDB 3l2t chain B

3D model

Region: 231 - 375
Aligned: 141
Modelled: 145
Confidence: 99.7%
Identity: 19%
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 1bco chain A domain 2

3D model

Region: 226 - 382
Aligned: 156
Modelled: 157
Confidence: 99.7%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2

PDB 1cxq chain A

3D model

Region: 231 - 360
Aligned: 124
Modelled: 130
Confidence: 99.7%
Identity: 19%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3dlr chain A

3D model

Region: 231 - 375
Aligned: 133
Modelled: 145
Confidence: 99.6%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase

Phyre2

PDB 1bco chain A

3D model

Region: 222 - 382
Aligned: 161
Modelled: 161
Confidence: 99.5%
Identity: 16%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 3hos chain A

3D model

Region: 7 - 366
Aligned: 290
Modelled: 293
Confidence: 99.2%
Identity: 11%
PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg

Phyre2

PDB 1u78 chain A

3D model

Region: 5 - 99
Aligned: 95
Modelled: 95
Confidence: 99.0%
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 2jn6 chain A domain 1

3D model

Region: 1 - 87
Aligned: 85
Modelled: 87
Confidence: 98.6%
Identity: 27%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Cgl2762-like

Phyre2
1

d1exqa_
2

c3f9kV_
3

d1c6va_
4

d1hyva_
5

c1ex4A_
6

c3nf9A_
7

d1c0ma2
8

c3kksB_
9

d1asua_
10

c3hpgC_
11

c1c0mA_
12

c1k6yB_
13

c3l2tB_
14

d1bcoa2
15

d1cxqa_
16

c3dlrA_
17

c1bcoA_
18

c3hosA_
19

c1u78A_
20

d2jn6a1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1exqa_



99.9 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
2c3f9kV_



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
3d1c6va_



99.9 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
4d1hyva_



99.9 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
5c1ex4A_



99.9 16 PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
6c3nf9A_



99.9 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
7d1c0ma2



99.8 20 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
8c3kksB_



99.8 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
9d1asua_



99.8 19 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
10c3hpgC_



99.8 18 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
11c1c0mA_



99.8 20 PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
12c1k6yB_



99.8 15 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
13c3l2tB_



99.7 19 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)
14d1bcoa2



99.7 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
15d1cxqa_



99.7 19 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
16c3dlrA_



99.6 17 PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
17c1bcoA_



99.5 16 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
18c3hosA_



99.2 11 PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
19c1u78A_



99.0 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
20d2jn6a1



98.6 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
21c6paxA_



not modelled 98.5 23 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
22d1pdnc_



not modelled 98.4 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
23c2rn7A_



not modelled 97.9 19 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
24c2k27A_



not modelled 97.7 11 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
25c2elhA_



not modelled 97.5 17 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
26c1hlvA_



not modelled 97.4 21 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
27d1k78a1



not modelled 97.3 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
28d1bw6a_



not modelled 97.0 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
29d6paxa1



not modelled 97.0 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
30d1hlva1



not modelled 97.0 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
31c3hefB_



not modelled 96.4 18 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
32d2coba1



not modelled 96.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
33d1tc3c_



not modelled 96.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
34d1q06a_



not modelled 96.0 14 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
35c2zhhA_



not modelled 96.0 12 PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr
36c2vz4A_



not modelled 95.9 10 PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional activator tipa;
PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna
37c3gp4B_



not modelled 95.3 20 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes
38c2jmlA_



not modelled 95.3 16 PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor
39d2ao9a1



not modelled 95.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
40d1r8da_



not modelled 95.2 13 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
41c1bdhA_



not modelled 95.2 21 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
42c3hh0C_



not modelled 95.1 11 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
43c3mklB_



not modelled 95.0 14 PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
44d1fsea_



not modelled 95.0 26 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)
45d1ijwc_



not modelled 94.9 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
46c3gpvA_



not modelled 94.9 10 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
47c3mn2B_



not modelled 94.9 14 PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
48d1vz0a1



not modelled 94.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
49d1xsva_



not modelled 94.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
50c3sztB_



not modelled 94.7 16 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
51c3oouA_



not modelled 94.7 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua
52d1or7a1



not modelled 94.7 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
53c3lsgD_



not modelled 94.7 15 PDB header:transcription regulator
Chain: D: PDB Molecule:two-component response regulator yesn;
PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586
54c1zvvA_



not modelled 94.6 16 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
55d1hcra_



not modelled 94.6 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
56c3hugA_



not modelled 94.5 27 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
57d1qpza1



not modelled 94.5 27 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
58d1rp3a2



not modelled 94.5 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
59c3frwF_



not modelled 94.4 36 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
60c2gm4B_



not modelled 94.3 14 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
61c2r0qF_



not modelled 94.3 21 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
62c1zljE_



not modelled 94.2 14 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
63d1efaa1



not modelled 94.2 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
64d2bjca1



not modelled 94.2 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
65c2o8xA_



not modelled 94.2 17 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
66c1bl0A_



not modelled 94.1 13 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
67d1s7oa_



not modelled 94.1 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
68d1a04a1



not modelled 93.9 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)
69d2hsga1



not modelled 93.9 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
70c2krfB_



not modelled 93.9 19 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
71c3korD_



not modelled 93.8 27 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
72c3gbgA_



not modelled 93.7 14 PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395
73c3qaoA_



not modelled 93.7 11 PDB header:transcription regulator
Chain: A: PDB Molecule:merr-like transcriptional regulator;
PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e
74c1r71B_



not modelled 93.7 22 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
75c3mzyA_



not modelled 93.7 21 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
76c2q0oA_



not modelled 93.6 19 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
77c1h0mD_



not modelled 93.6 24 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
78d1llib_



not modelled 93.6 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
79d1r71a_



not modelled 93.5 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
80c1x3uA_



not modelled 93.5 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
81d1r8ea1



not modelled 93.5 7 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
82c2x4hA_



not modelled 93.5 14 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
83c2ao9H_



not modelled 93.5 25 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
84c3kjxD_



not modelled 93.3 28 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
85d1l3la1



not modelled 93.2 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)
86c3oioA_



not modelled 93.1 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum
87c2w48D_



not modelled 93.0 21 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
88c2jpcA_



not modelled 92.7 19 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
89d1yioa1



not modelled 92.7 22 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)
90d1p4wa_



not modelled 92.6 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)
91c1y9qA_



not modelled 92.6 27 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, hth_3 family;
PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
92c1or7A_



not modelled 92.6 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
93c3e7lD_



not modelled 92.6 10 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
94d1fipa_



not modelled 92.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
95c2k9sA_



not modelled 92.5 13 PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac
96d1ntca_



not modelled 92.5 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
97c3h5tA_



not modelled 92.5 22 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
98c2rnjA_



not modelled 92.4 20 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
99d1jhga_



not modelled 92.3 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
100c3fmyA_



not modelled 92.3 17 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)
101d1uxda_



not modelled 92.2 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
102c3cloC_



not modelled 92.2 19 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
103d1g2ha_



not modelled 92.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
104d2b5aa1



not modelled 92.1 25 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
105d1trra_



not modelled 91.8 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
106c3qp5C_



not modelled 91.7 22 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
107d1etxa_



not modelled 91.7 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
108d1lmb3_



not modelled 91.5 22 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
109c2x48B_



not modelled 91.3 29 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
110d1umqa_



not modelled 91.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
111c1umqA_



not modelled 91.2 16 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
112c3bdnB_



not modelled 91.2 17 PDB header:transcription/dna
Chain: B: PDB Molecule:lambda repressor;
PDBTitle: crystal structure of the lambda repressor
113d1rioa_



not modelled 91.1 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
114c1rp3G_



not modelled 91.1 20 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
115c2dg6A_



not modelled 91.0 21 PDB header:gene regulation
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator sco55502 from streptomyces coelicolor a3(2)
116c3c3wB_



not modelled 90.9 14 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
117c2kpjA_



not modelled 90.9 21 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
118c2it0A_



not modelled 90.9 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
119c1rnlA_



not modelled 90.8 17 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
120d2ofya1



not modelled 90.7 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like

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