Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP19769
DateThu Jan 5 11:37:35 GMT 2012
Unique Job ID0a17b381faf220ee

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: 99.7% Coverage: 51%
143 residues ( 51% of your sequence) have been modelled with 99.7% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
271 residues ( 96%) 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  MKVLNELRQFYPLDELLRAAEIPRSTFYYHLKALSKPDKYADVKKRISEIYHENRGRYGY
Secondary structure 

















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Disorder  ?





























????????




















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   .........70.........80.........90.........100.........110.........120
Sequence  RRVTLSLHREGKQINHKAVQRLMGTLSLKAAIKVKRYRSYRGEVGQTAPNVLQRDFKATR
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?????

?

















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   .........130.........140.........150.........160.........170.........180
Sequence  PNEKWVTDVTEFAVNGRKLYLSPVIDLFNNEVISYSLSERPVMNMVENMLDQAFKKLNPH
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   .........190.........200.........210.........220.........230.........240
Sequence  EHPVLHSDQGWQYRMRRYQNILKEHGIKQSMSRKGNCLDNAVVECFFGTLKSECFYLDEF
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   .........250.........260.........270.........280...
Sequence  SNISELKDAVTEYIEYYNSRRISLKLKGLTPIEYRNQTYMPRV
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 3f9k chain V

3D model

Region: 120 - 273
Aligned: 143
Modelled: 154
Confidence: 99.7%
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 1bco chain A domain 2

3D model

Region: 120 - 281
Aligned: 162
Modelled: 162
Confidence: 99.6%
Identity: 14%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2

PDB 1c0m chain A domain 2

3D model

Region: 120 - 273
Aligned: 149
Modelled: 154
Confidence: 99.6%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1asu chain A

3D model

Region: 120 - 271
Aligned: 147
Modelled: 152
Confidence: 99.6%
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 - 273
Aligned: 151
Modelled: 156
Confidence: 99.6%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2

PDB 1exq chain A

3D model

Region: 120 - 280
Aligned: 142
Modelled: 161
Confidence: 99.5%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 122 - 274
Aligned: 142
Modelled: 153
Confidence: 99.5%
Identity: 18%
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 1ex4 chain A

3D model

Region: 120 - 274
Aligned: 141
Modelled: 155
Confidence: 99.4%
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: 123 - 277
Aligned: 143
Modelled: 155
Confidence: 99.3%
Identity: 21%
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 1k6y chain B

3D model

Region: 114 - 273
Aligned: 140
Modelled: 160
Confidence: 99.3%
Identity: 15%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2

PDB 1bco chain A

3D model

Region: 123 - 283
Aligned: 160
Modelled: 161
Confidence: 99.3%
Identity: 14%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 1hyv chain A

3D model

Region: 122 - 277
Aligned: 133
Modelled: 156
Confidence: 99.3%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1c6v chain A

3D model

Region: 124 - 273
Aligned: 128
Modelled: 150
Confidence: 99.3%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1cxq chain A

3D model

Region: 120 - 259
Aligned: 133
Modelled: 140
Confidence: 99.3%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3hos chain A

3D model

Region: 3 - 255
Aligned: 243
Modelled: 253
Confidence: 99.2%
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 3hpg chain C

3D model

Region: 120 - 274
Aligned: 143
Modelled: 155
Confidence: 99.1%
Identity: 17%
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 3l2t chain B

3D model

Region: 118 - 273
Aligned: 149
Modelled: 156
Confidence: 99.1%
Identity: 21%
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 3dlr chain A

3D model

Region: 119 - 273
Aligned: 138
Modelled: 155
Confidence: 98.6%
Identity: 22%
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 - 87
Aligned: 86
Modelled: 86
Confidence: 97.9%
Identity: 12%
PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions

Phyre2

PDB 1u78 chain A

3D model

Region: 2 - 87
Aligned: 82
Modelled: 86
Confidence: 97.6%
Identity: 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

Phyre2
1

c3f9kV_
2

d1bcoa2
3

d1c0ma2
4

d1asua_
5

c1c0mA_
6

d1exqa_
7

c3nf9A_
8

c1ex4A_
9

c3kksB_
10

c1k6yB_
11

c1bcoA_
12

d1hyva_
13

d1c6va_
14

d1cxqa_
15

c3hosA_
16

c3hpgC_
17

c3l2tB_
18

c3dlrA_
19

c6paxA_
20

c1u78A_
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Detailed template information 

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



99.7 18 PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
2d1bcoa2



99.6 14 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
3d1c0ma2



99.6 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
4d1asua_



99.6 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
5c1c0mA_



99.6 17 PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
6d1exqa_



99.5 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
7c3nf9A_



99.5 18 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
8c1ex4A_



99.4 18 PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
9c3kksB_



99.3 21 PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii
10c1k6yB_



99.3 15 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
11c1bcoA_



99.3 14 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
12d1hyva_



99.3 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
13d1c6va_



99.3 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
14d1cxqa_



99.3 18 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
15c3hosA_



99.2 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
16c3hpgC_



99.1 17 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
17c3l2tB_



99.1 21 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)
18c3dlrA_



98.6 22 PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
19c6paxA_



97.9 12 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
20c1u78A_



97.6 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
21d1pdnc_



not modelled 97.6 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
22c2f7tA_



not modelled 97.3 11 PDB header:dna binding protein
Chain: A: PDB Molecule:mos1 transposase;
PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase
23c3f2kB_



not modelled 97.3 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
24c2k27A_



not modelled 97.0 9 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
25d2jn6a1



not modelled 96.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
26c1hlvA_



not modelled 95.9 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
27c3hefB_



not modelled 95.4 16 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
28c2elhA_



not modelled 95.3 16 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
29c1umqA_



not modelled 94.3 18 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
30d1umqa_



not modelled 94.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
31d1g2ha_



not modelled 93.1 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
32d1fipa_



not modelled 93.0 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
33d1rzsa_



not modelled 92.8 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
34d1etxa_



not modelled 92.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
35d1ntca_



not modelled 92.4 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
36c1z4hA_



not modelled 92.0 17 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
37c3bd1B_



not modelled 91.3 11 PDB header:transcription
Chain: B: PDB Molecule:cro protein;
PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1
38d1k78a1



not modelled 91.3 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
39c3e7lD_



not modelled 91.2 27 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
40d2coba1



not modelled 91.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
41c3fmyA_



not modelled 90.8 8 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)
42d1etob_



not modelled 90.7 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
43c3bs3A_



not modelled 90.5 14 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
44d6paxa1



not modelled 90.5 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
45d1hlva1



not modelled 90.2 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
46d1utxa_



not modelled 90.2 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
47d1adra_



not modelled 89.9 5 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
48c3cecA_



not modelled 89.8 5 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
49d2icta1



not modelled 89.7 26 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
50c2xcjB_



not modelled 89.3 16 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
51d1y9qa1



not modelled 89.3 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
52c3omtA_



not modelled 89.0 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.
53c2kpjA_



not modelled 89.0 16 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
54c2rn7A_



not modelled 88.9 8 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
55d1llib_



not modelled 88.9 7 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
56d2ppxa1



not modelled 88.3 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
57c2ppxA_



not modelled 88.3 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein atu1735;
PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens
58d2b5aa1



not modelled 88.1 13 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
59c3b7hA_



not modelled 88.0 19 PDB header:structural protein
Chain: A: PDB Molecule:prophage lp1 protein 11;
PDBTitle: crystal structure of the prophage lp1 protein 11
60d2id3a1



not modelled 87.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
61d1t56a1



not modelled 87.8 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
62d2fbqa1



not modelled 87.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
63c2ebyA_



not modelled 87.1 11 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli
64c3f52A_



not modelled 87.0 14 PDB header:transcription activator
Chain: A: PDB Molecule:clp gene regulator (clgr);
PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
65c2iu5A_



not modelled 87.0 18 PDB header:transcription
Chain: A: PDB Molecule:hth-type dhaklm operon transcriptional activator dhas;
PDBTitle: dihydroxyacetone kinase operon activator dhas
66c3clcC_



not modelled 86.9 8 PDB header:transcription regulator/dna
Chain: C: PDB Molecule:regulatory protein;
PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator
67c3kjxD_



not modelled 86.9 15 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
68c3h5tA_



not modelled 86.9 17 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
69c3eusB_



not modelled 86.8 16 PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding protein;
PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
70c2fjrB_



not modelled 86.8 15 PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186
71c3b81A_



not modelled 86.7 15 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
72d1lmb3_



not modelled 86.6 5 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
73c3o60A_



not modelled 86.5 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin0861 protein;
PDBTitle: the crystal structure of lin0861 from listeria innocua to 2.8a
74d2fd5a1



not modelled 86.5 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
75c2jvlA_



not modelled 86.2 19 PDB header:transcription
Chain: A: PDB Molecule:trmbf1;
PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
76c3kkcB_



not modelled 86.1 23 PDB header:transcription regulator
Chain: B: PDB Molecule:tetr family transcriptional regulator;
PDBTitle: the crystal structure of tetr transcriptional regulator from2 streptococcus agalactiae 2603v
77d2bjca1



not modelled 86.0 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
78d2np5a1



not modelled 85.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
79d2vkva1



not modelled 85.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
80c3op9A_



not modelled 85.7 13 PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua
81d2ao9a1



not modelled 85.6 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
82c3gn5B_



not modelled 85.6 8 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)
83c3ppbB_



not modelled 85.5 18 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
84d2fq4a1



not modelled 85.4 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
85c3t76A_



not modelled 85.3 28 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator vanug;
PDBTitle: crystal structure of transcriptional regulator vanug, form ii
86c2ibdB_



not modelled 85.2 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:possible transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulatory protein2 rha5900
87c3f1bA_



not modelled 85.2 23 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.
88c1vi0B_



not modelled 85.2 18 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator
89d1j5ya1



not modelled 85.0 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
90c3ivpD_



not modelled 85.0 14 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.
91d2iu5a1



not modelled 84.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
92d2oi8a1



not modelled 84.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
93d1jt6a1



not modelled 84.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
94d2vkea1



not modelled 84.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
95c3trbA_



not modelled 84.7 11 PDB header:dna binding protein
Chain: A: PDB Molecule:virulence-associated protein i;
PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii
96d1pb6a1



not modelled 84.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
97d1rkta1



not modelled 84.5 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
98d1r8da_



not modelled 84.5 10 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
99d3c07a1



not modelled 84.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
100c2l0kA_



not modelled 84.3 15 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
101d1z0xa1



not modelled 84.1 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
102c2ef8A_



not modelled 84.0 16 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcription factor;
PDBTitle: crystal structure of c.ecot38is
103c3he0A_



not modelled 84.0 18 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: the structure of a putative transcriptional regulator tetr family2 protein from vibrio parahaemolyticus.
104d1vi0a1



not modelled 83.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
105d1zk8a1



not modelled 83.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
106d1v7ba1



not modelled 83.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
107d2ofya1



not modelled 83.9 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
108d1mkma1



not modelled 83.7 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
109c3pasA_



not modelled 83.7 15 PDB header:transcription regulator
Chain: A: PDB Molecule:tetr family transcription regulator;
PDBTitle: crystal structure of a tetr family transcription regulator (maqu_1417)2 from marinobacter aquaeolei vt8 at 1.90 a resolution
110c2lcvA_



not modelled 83.6 12 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional repressor cytr;
PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
111c2iaiA_



not modelled 83.6 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative transcriptional regulator sco3833;
PDBTitle: crystal structure of sco3833, a member of the tetr transcriptional2 regulator family from streptomyces coelicolor a3
112d2g3ba1



not modelled 83.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
113d2o7ta1



not modelled 83.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
114c2eh3A_



not modelled 83.5 18 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of aq_1058, a transcriptional regulator (terr/acrr2 family) from aquifex aeolicus vf5
115c3gpvA_



not modelled 83.4 15 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
116c2guhA_



not modelled 83.4 9 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
117c1bdhA_



not modelled 83.4 8 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
118d1y7ya1



not modelled 83.3 10 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
119c1bjzA_



not modelled 83.3 20 PDB header:transcription regulation
Chain: A: PDB Molecule:tetracycline repressor;
PDBTitle: tetracycline chelated mg2+-ion initiates helix unwinding for tet2 repressor induction
120d1x57a1



not modelled 83.3 8 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:EDF1-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
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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