Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP14294
DateThu Jan 5 11:33:58 GMT 2012
Unique Job ID2c438031f6db000e

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2o59B_
Top template information
PDB header:isomerase/dna
Chain: B: PDB Molecule:dna topoisomerase 3;
PDBTitle: structure of e. coli topoisomerase iii in complex with an 8-2 base single stranded oligonucleotide. frozen in glycerol3 ph 8.0
Confidence and coverage
Confidence:100.0% Coverage: 96%
625 residues ( 96% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYAR
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Disorder  ?


















????
?























?????
?


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   .........70.........80.........90.........100.........110.........120
Sequence  WNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQ
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   .........130.........140.........150.........160.........170.........180
Sequence  LAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAY
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?

?

























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




??
?

?





















?
























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



??
























?







???????












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   .........310.........320.........330.........340.........350.........360
Sequence  AAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLP
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   .........370.........380.........390.........400.........410.........420
Sequence  QPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVF
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??????
?????????








???????























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   .........430.........440.........450.........460.........470.........480
Sequence  RKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEV
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????????















???
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   .........490.........500.........510.........520.........530.........540
Sequence  VERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGF
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Disorder  ????
?






























?????
?















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   .........550.........560.........570.........580.........590.........600
Sequence  LTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLY
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???














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   .........610.........620.........630.........640.........650...
Sequence  QLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKSPPADEVGSGAIA
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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 2o59 chain B

3D model

Region: 1 - 625
Aligned: 625
Modelled: 625
Confidence: 100.0%
Identity: 99%
PDB header:isomerase/dna
Chain: B: PDB Molecule:dna topoisomerase 3;
PDBTitle: structure of e. coli topoisomerase iii in complex with an 8-2 base single stranded oligonucleotide. frozen in glycerol3 ph 8.0

Phyre2

PDB 1i7d chain A

3D model

Region: 1 - 620
Aligned: 620
Modelled: 620
Confidence: 100.0%
Identity: 100%
Fold: Prokaryotic type I DNA topoisomerase
Superfamily: Prokaryotic type I DNA topoisomerase
Family: Prokaryotic type I DNA topoisomerase

Phyre2

PDB 1mw9 chain X

3D model

Region: 2 - 614
Aligned: 541
Modelled: 562
Confidence: 100.0%
Identity: 24%
Fold: Prokaryotic type I DNA topoisomerase
Superfamily: Prokaryotic type I DNA topoisomerase
Family: Prokaryotic type I DNA topoisomerase

Phyre2

PDB 2gaj chain A

3D model

Region: 2 - 653
Aligned: 562
Modelled: 588
Confidence: 100.0%
Identity: 21%
PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form

Phyre2

PDB 1gku chain B domain 3

3D model

Region: 1 - 602
Aligned: 500
Modelled: 526
Confidence: 100.0%
Identity: 21%
Fold: Prokaryotic type I DNA topoisomerase
Superfamily: Prokaryotic type I DNA topoisomerase
Family: Prokaryotic type I DNA topoisomerase

Phyre2

PDB 1gl9 chain B

3D model

Region: 1 - 602
Aligned: 502
Modelled: 529
Confidence: 100.0%
Identity: 22%
PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp

Phyre2

PDB 1cy9 chain A

3D model

Region: 216 - 487
Aligned: 241
Modelled: 258
Confidence: 100.0%
Identity: 24%
Fold: Prokaryotic type I DNA topoisomerase
Superfamily: Prokaryotic type I DNA topoisomerase
Family: Prokaryotic type I DNA topoisomerase

Phyre2

PDB 1vdd chain A

3D model

Region: 2 - 154
Aligned: 107
Modelled: 110
Confidence: 98.9%
Identity: 15%
Fold: Recombination protein RecR
Superfamily: Recombination protein RecR
Family: Recombination protein RecR

Phyre2

PDB 1vdd chain C

3D model

Region: 2 - 153
Aligned: 103
Modelled: 103
Confidence: 98.6%
Identity: 19%
PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr

Phyre2

PDB 2x4h chain A

3D model

Region: 497 - 628
Aligned: 117
Modelled: 132
Confidence: 95.6%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus

Phyre2

PDB 1s3j chain A

3D model

Region: 492 - 583
Aligned: 71
Modelled: 71
Confidence: 94.7%
Identity: 8%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2

PDB 3boq chain B

3D model

Region: 524 - 607
Aligned: 73
Modelled: 84
Confidence: 94.3%
Identity: 21%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcriptional regulator from2 silicibacter pomeroyi

Phyre2

PDB 2fcj chain A domain 1

3D model

Region: 2 - 150
Aligned: 93
Modelled: 101
Confidence: 93.5%
Identity: 19%
Fold: Toprim domain
Superfamily: Toprim domain
Family: Toprim domain

Phyre2

PDB 3nrv chain C

3D model

Region: 524 - 583
Aligned: 60
Modelled: 60
Confidence: 93.4%
Identity: 17%
PDB header:transcription regulator
Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family);
PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1

Phyre2

PDB 2pex chain A

3D model

Region: 524 - 602
Aligned: 70
Modelled: 79
Confidence: 93.3%
Identity: 24%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator ohrr;
PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris

Phyre2

PDB 1r7j chain A

3D model

Region: 530 - 581
Aligned: 52
Modelled: 52
Confidence: 92.8%
Identity: 12%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Archaeal DNA-binding protein

Phyre2

PDB 1lnw chain A

3D model

Region: 489 - 585
Aligned: 76
Modelled: 76
Confidence: 92.5%
Identity: 21%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2

PDB 2eth chain A domain 1

3D model

Region: 489 - 583
Aligned: 74
Modelled: 75
Confidence: 92.4%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2

PDB 3f3x chain A

3D model

Region: 524 - 602
Aligned: 70
Modelled: 79
Confidence: 92.1%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus

Phyre2

PDB 3s2w chain B

3D model

Region: 524 - 609
Aligned: 75
Modelled: 86
Confidence: 91.6%
Identity: 15%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the crystal structure of a marr transcriptional regulator from2 methanosarcina mazei go1

Phyre2
1

c2o59B_
2

d1i7da_
3

d1mw9x_
4

c2gajA_
5

d1gkub3
6

c1gl9B_
7

d1cy9a_
8

d1vdda_
9

c1vddC_
10

c2x4hA_
11

d1s3ja_
12

c3boqB_
13

d2fcja1
14

c3nrvC_
15

c2pexA_
16

d1r7ja_
17

d1lnwa_
18

d2etha1
19

c3f3xA_
20

c3s2wB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2o59B_



100.0 99 PDB header:isomerase/dna
Chain: B: PDB Molecule:dna topoisomerase 3;
PDBTitle: structure of e. coli topoisomerase iii in complex with an 8-2 base single stranded oligonucleotide. frozen in glycerol3 ph 8.0
2d1i7da_



100.0 100 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
3d1mw9x_



100.0 24 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
4c2gajA_



100.0 21 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form
5d1gkub3



100.0 21 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
6c1gl9B_



100.0 22 PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp
7d1cy9a_



100.0 24 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
8d1vdda_



98.9 15 Fold:Recombination protein RecR
Superfamily:Recombination protein RecR
Family:Recombination protein RecR
9c1vddC_



98.6 19 PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr
10c2x4hA_



95.6 13 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
11d1s3ja_



94.7 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
12c3boqB_



94.3 21 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcriptional regulator from2 silicibacter pomeroyi
13d2fcja1



93.5 19 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
14c3nrvC_



93.4 17 PDB header:transcription regulator
Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family);
PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1
15c2pexA_



93.3 24 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator ohrr;
PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris
16d1r7ja_



92.8 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Archaeal DNA-binding protein
17d1lnwa_



92.5 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
18d2etha1



92.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
19c3f3xA_



92.1 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
20c3s2wB_



91.6 15 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the crystal structure of a marr transcriptional regulator from2 methanosarcina mazei go1
21c3kp3B_



not modelled 91.5 14 PDB header:transcription regulator/antibiotic
Chain: B: PDB Molecule:transcriptional regulator tcar;
PDBTitle: staphylococcus epidermidis in complex with ampicillin
22c2fa5B_



not modelled 91.5 12 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator marr/emrr family;
PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris
23d3broa1



not modelled 91.3 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
24c3g3zA_



not modelled 91.2 22 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
25d1lj9a_



not modelled 90.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
26c3bj6B_



not modelled 90.7 12 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
27c3e6mD_



not modelled 90.6 22 PDB header:transcription regulator
Chain: D: PDB Molecule:marr family transcriptional regulator;
PDBTitle: the crystal structure of a marr family transcriptional2 regulator from silicibacter pomeroyi dss.
28c2rdpA_



not modelled 90.5 12 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
29d2fbka1



not modelled 90.3 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
30c2qwwB_



not modelled 90.1 13 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution
31d3ctaa1



not modelled 90.0 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
32c3bjaA_



not modelled 89.6 13 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of putative marr-like transcription regulator2 (np_978771.1) from bacillus cereus atcc 10987 at 2.38 a resolution
33d2bv6a1



not modelled 89.6 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
34d2fxaa1



not modelled 89.6 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
35c3fm5D_



not modelled 89.2 20 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator;
PDBTitle: x-ray crystal structure of transcriptional regulator (marr family)2 from rhodococcus sp. rha1
36c3hrmA_



not modelled 88.8 21 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator sarz;
PDBTitle: crystal structure of staphylococcus aureus protein sarz in sulfenic2 acid form
37c2fxaB_



not modelled 88.7 18 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
38c3ecoB_



not modelled 88.6 19 PDB header:transcription
Chain: B: PDB Molecule:mepr;
PDBTitle: crystal structure of mepr, a transcription regulator of the2 staphylococcus aureus multidrug efflux pump mepa
39d2fbia1



not modelled 88.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
40c2nyxB_



not modelled 88.3 18 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
41c1g3wA_



not modelled 87.9 15 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
42d1t6t1_



not modelled 87.8 15 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
43d1jgsa_



not modelled 87.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
44c3hruA_



not modelled 87.2 15 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
45c3r0aB_



not modelled 86.9 14 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
46c1f5tA_



not modelled 86.6 15 PDB header:transcription/dna
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
47d1ub9a_



not modelled 86.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
48d1stza1



not modelled 85.6 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
49d2hr3a1



not modelled 85.6 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
50c2ev5B_



not modelled 85.4 24 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
51d1p4xa1



not modelled 85.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
52c3cjnA_



not modelled 85.0 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
53d1p4xa2



not modelled 84.7 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
54c1fx7C_



not modelled 84.0 20 PDB header:signaling protein
Chain: C: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of the iron-dependent regulator (ider)2 from mycobacterium tuberculosis
55c3nqoB_



not modelled 83.9 17 PDB header:transcription
Chain: B: PDB Molecule:marr-family transcriptional regulator;
PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
56c2nnnB_



not modelled 83.7 26 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
57c2gxgA_



not modelled 83.7 12 PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
58c3k0lA_



not modelled 83.3 13 PDB header:transcription regulator
Chain: A: PDB Molecule:repressor protein;
PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
59d1z91a1



not modelled 83.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
60c3tgnA_



not modelled 83.1 19 PDB header:transcription
Chain: A: PDB Molecule:adc operon repressor adcr;
PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state
61c1nuiA_



not modelled 83.0 16 PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein
62c3bpxB_



not modelled 82.6 20 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of marr
63d1hsja1



not modelled 82.5 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
64d2a61a1



not modelled 81.5 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
65d2fbha1



not modelled 81.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
66c1p4xA_



not modelled 81.3 17 PDB header:transcription
Chain: A: PDB Molecule:staphylococcal accessory regulator a homologue;
PDBTitle: crystal structure of sars protein from staphylococcus aureus
67d2fnaa1



not modelled 81.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Helicase DNA-binding domain
68d1nuia1



not modelled 80.1 16 Fold:DNA primase core
Superfamily:DNA primase core
Family:Primase fragment of primase-helicase protein
69c2h09A_



not modelled 79.7 23 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
70c3nuhB_



not modelled 79.3 14 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: a domain insertion in e. coli gyrb adopts a novel fold that plays a2 critical role in gyrase function
71c3cdhB_



not modelled 78.4 28 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of the marr family transcriptional regulator spo14532 from silicibacter pomeroyi dss-3
72c2it0A_



not modelled 77.3 21 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
73c3jw4C_



not modelled 76.5 19 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, marr/emrr family;
PDBTitle: the structure of a putative marr family transcriptional regulator from2 clostridium acetobutylicum
74c3ctaA_



not modelled 76.0 21 PDB header:transferase
Chain: A: PDB Molecule:riboflavin kinase;
PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
75d1olta_



not modelled 75.7 16 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:Oxygen-independent coproporphyrinogen III oxidase HemN
76c1ylmA_



not modelled 74.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein bsu32300;
PDBTitle: structure of cytosolic protein of unknown function yute2 from bacillus subtilis
77c3oopA_



not modelled 74.0 23 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2960 protein;
PDBTitle: the structure of a protein with unknown function from listeria innocua2 clip11262
78c2wteB_



not modelled 72.9 29 PDB header:antiviral protein
Chain: B: PDB Molecule:csa3;
PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
79c1t98B_



not modelled 69.0 11 PDB header:cell cycle
Chain: B: PDB Molecule:chromosome partition protein mukf;
PDBTitle: crystal structure of mukf(1-287)
80d1okra_



not modelled 68.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
81d1ku9a_



not modelled 67.5 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
82c3fofD_



not modelled 67.1 18 PDB header:isomerase/dna
Chain: D: PDB Molecule:dna topoisomerase 4 subunit b;
PDBTitle: structural insight into the quinolone-dna cleavage complex2 of type iia topoisomerases
83c1q57G_



not modelled 67.0 19 PDB header:transferase
Chain: G: PDB Molecule:dna primase/helicase;
PDBTitle: the crystal structure of the bifunctional primase-helicase of2 bacteriophage t7
84c3l7wA_



not modelled 66.2 24 PDB header:transcription
Chain: A: PDB Molecule:putative uncharacterized protein smu.1704;
PDBTitle: the crystal structure of smu.1704 from streptococcus mutans ua159
85d2esna1



not modelled 66.2 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LysR-like transcriptional regulators
86d2isya1



not modelled 65.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
87c3deuB_



not modelled 64.5 14 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator slya;
PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands
88d2hyec1



not modelled 63.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:SCF ubiquitin ligase complex WHB domain
89c1byvA_



not modelled 62.2 69 PDB header:hormone/growth factor
Chain: A: PDB Molecule:protein (calcitonin);
PDBTitle: glycosylated eel calcitonin
90d1jhfa1



not modelled 61.6 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
91c3bddD_



not modelled 61.0 17 PDB header:transcription
Chain: D: PDB Molecule:regulatory protein marr;
PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution
92d1g3wa1



not modelled 60.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
93c3m1eA_



not modelled 56.8 11 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator benm;
PDBTitle: crystal structure of benm_dbd
94d1mkma1



not modelled 56.7 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
95c3u1dA_



not modelled 55.2 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: the structure of a protein with a gntr superfamily winged-helix-turn-2 helix domain from halomicrobium mukohataei.
96d1iuya_



not modelled 52.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:SCF ubiquitin ligase complex WHB domain
97d3deua1



not modelled 51.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
98d1q1ha_



not modelled 51.0 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcription factor E/IIe-alpha, N-terminal domain
99c1q1hA_



not modelled 51.0 16 PDB header:transcription
Chain: A: PDB Molecule:transcription factor e;
PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha
100d1ldja1



not modelled 50.7 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:SCF ubiquitin ligase complex WHB domain
101d2ev0a1



not modelled 48.6 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
102c2k4bA_



not modelled 46.0 7 PDB header:dna binding protein
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: copr repressor structure
103c2au3A_



not modelled 44.6 15 PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: crystal structure of the aquifex aeolicus primase (zinc binding and2 rna polymerase domains)
104c2vn2B_



not modelled 44.6 24 PDB header:replication
Chain: B: PDB Molecule:chromosome replication initiation protein;
PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426
105d1yg2a_



not modelled 44.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PadR-like
106c2zjtB_



not modelled 43.1 31 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: crystal structure of dna gyrase b' domain sheds lights on2 the mechanism for t-segment navigation
107c4a0lH_



not modelled 42.8 15 PDB header:ligase/dna-binding protein/dna
Chain: H: PDB Molecule:cullin-4b;
PDBTitle: structure of ddb1-ddb2-cul4b-rbx1 bound to a 12 bp abasic2 site containing dna-duplex
108d2frha1



not modelled 42.4 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
109c3ri2B_



not modelled 40.7 22 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, padr-like family;
PDBTitle: crystal structure of padr family transcriptional regulator from2 eggerthella lenta dsm 2243
110c3hhhA_



not modelled 39.5 25 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, padr family;
PDBTitle: crystal structure of transcriptional regulator, a member of padr2 family, from enterococcus faecalis v583
111c2uvgA_



not modelled 39.2 14 PDB header:sugar-binding protein
Chain: A: PDB Molecule:abc type periplasmic sugar-binding protein;
PDBTitle: structure of a periplasmic oligogalacturonide binding2 protein from yersinia enterocolitica
112d1bjaa_



not modelled 37.6 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcription factor MotA, activation domain
113d2cg4a1



not modelled 36.8 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
114d1p6ra_



not modelled 35.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
115c3l09B_



not modelled 35.2 19 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator2 (jann_22dec04_contig27_revised_gene3569) from jannaschia sp. ccs1 at3 2.81 a resolution
116d2p6ra1



not modelled 34.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:RecQ helicase DNA-binding domain-like
117c2hyeC_



not modelled 34.3 13 PDB header:protein binding
Chain: C: PDB Molecule:cullin-4a;
PDBTitle: crystal structure of the ddb1-cul4a-rbx1-sv5v complex
118c3okqA_



not modelled 33.9 24 PDB header:protein binding
Chain: A: PDB Molecule:bud site selection protein 6;
PDBTitle: crystal structure of a core domain of yeast actin nucleation cofactor2 bud6
119c2x8qA_



not modelled 32.7 18 PDB header:virus
Chain: A: PDB Molecule:capsid protein p27;
PDBTitle: cryo-em 3d model of the icosahedral particle2 composed of rous sarcoma virus capsid protein pentamers
120d2d1ha1



not modelled 32.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-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