Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP06612
DateThu Jan 5 10:59:12 GMT 2012
Unique Job ID0c63925047a9258c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1mw9x_
Top template information
Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
Confidence and coverage
Confidence:100.0% Coverage: 64%
555 residues ( 64% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
774 residues ( 89%) 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  MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPK
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Disorder  ???


















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?

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   .........70.........80.........90.........100.........110.........120
Sequence  KDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIA
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Disorder 
????






















































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   .........130.........140.........150.........160.........170.........180
Sequence  WHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS
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??






















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





?
























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   .........250.........260.........270.........280.........290.........300
Sequence  QNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFG
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???????




















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   .........310.........320.........330.........340.........350.........360
Sequence  VKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKEN
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?


























?
???????
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   .........370.........380.........390.........400.........410.........420
Sequence  SQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDF
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Disorder  ????









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
















????
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   .........490.........500.........510.........520.........530.........540
Sequence  SLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNY
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   .........550.........560.........570.........580.........590.........600
Sequence  DFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCP
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???






























???


???


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   .........610.........620.........630.........640.........650.........660
Sequence  TCGRKMGIRTASTGVFLGCSGYALPPKERCKTTINLVPENEVLNVLEGEDAETNALRAKR
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?????????????
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   .........670.........680.........690.........700.........710.........720
Sequence  RCPKCGTAMDSYLIDPKRKLHVCGNNPTCDGYEIEEGEFRIKGYDGPIVECEKCGSEMHL
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?

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   .........730.........740.........750.........760.........770.........780
Sequence  KMGRFGKYMACTNEECKNTRKILRNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVF
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Disorder  ?




















?????




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   .........790.........800.........810.........820.........830.........840
Sequence  LAANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYV
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???????
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???



















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   .........850.........860.....
Sequence  SSEKDGKATGWSAFYVDGKWVEGKK
Secondary structure 












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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 1mw9 chain X

3D model

Region: 2 - 591
Aligned: 555
Modelled: 567
Confidence: 100.0%
Identity: 98%
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: 4 - 640
Aligned: 567
Modelled: 605
Confidence: 100.0%
Identity: 38%
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 2o59 chain B

3D model

Region: 4 - 605
Aligned: 568
Modelled: 583
Confidence: 100.0%
Identity: 25%
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: 4 - 600
Aligned: 563
Modelled: 563
Confidence: 100.0%
Identity: 25%
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 - 574
Aligned: 495
Modelled: 517
Confidence: 100.0%
Identity: 28%
PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp

Phyre2

PDB 1gku chain B domain 3

3D model

Region: 1 - 573
Aligned: 495
Modelled: 506
Confidence: 100.0%
Identity: 28%
Fold: Prokaryotic type I DNA topoisomerase
Superfamily: Prokaryotic type I DNA topoisomerase
Family: Prokaryotic type I DNA topoisomerase

Phyre2

PDB 1cy9 chain A

3D model

Region: 214 - 473
Aligned: 245
Modelled: 260
Confidence: 100.0%
Identity: 98%
Fold: Prokaryotic type I DNA topoisomerase
Superfamily: Prokaryotic type I DNA topoisomerase
Family: Prokaryotic type I DNA topoisomerase

Phyre2

PDB 1yua chain A

3D model

Region: 744 - 865
Aligned: 122
Modelled: 122
Confidence: 100.0%
Identity: 99%
PDB header:dna binding protein
Chain: A: PDB Molecule:topoisomerase i;
PDBTitle: c-terminal domain of escherichia coli topoisomerase i

Phyre2

PDB 1yua chain A domain 2

3D model

Region: 809 - 865
Aligned: 57
Modelled: 57
Confidence: 99.9%
Identity: 100%
Fold: Rubredoxin-like
Superfamily: Zinc beta-ribbon
Family: Prokaryotic DNA topoisomerase I, a C-terminal fragment

Phyre2

PDB 1yua chain A domain 1

3D model

Region: 744 - 808
Aligned: 65
Modelled: 65
Confidence: 99.4%
Identity: 98%
Fold: Rubredoxin-like
Superfamily: Zinc beta-ribbon
Family: Prokaryotic DNA topoisomerase I, a C-terminal fragment

Phyre2

PDB 1vdd chain A

3D model

Region: 2 - 160
Aligned: 110
Modelled: 113
Confidence: 99.2%
Identity: 25%
Fold: Recombination protein RecR
Superfamily: Recombination protein RecR
Family: Recombination protein RecR

Phyre2

PDB 1vdd chain C

3D model

Region: 2 - 158
Aligned: 108
Modelled: 111
Confidence: 99.0%
Identity: 25%
PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr

Phyre2

PDB 2fcj chain A domain 1

3D model

Region: 3 - 155
Aligned: 95
Modelled: 99
Confidence: 97.0%
Identity: 22%
Fold: Toprim domain
Superfamily: Toprim domain
Family: Toprim domain

Phyre2

PDB 1i3q chain I

3D model

Region: 599 - 750
Aligned: 104
Modelled: 114
Confidence: 96.5%
Identity: 13%
PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd
PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution

Phyre2

PDB 1nui chain A domain 1

3D model

Region: 1 - 150
Aligned: 96
Modelled: 98
Confidence: 95.8%
Identity: 21%
Fold: DNA primase core
Superfamily: DNA primase core
Family: Primase fragment of primase-helicase protein

Phyre2

PDB 3h0g chain I

3D model

Region: 599 - 739
Aligned: 93
Modelled: 103
Confidence: 95.6%
Identity: 17%
PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe

Phyre2

PDB 1nui chain A

3D model

Region: 2 - 150
Aligned: 95
Modelled: 97
Confidence: 95.2%
Identity: 21%
PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein

Phyre2

PDB 2x4h chain A

3D model

Region: 493 - 606
Aligned: 94
Modelled: 114
Confidence: 95.0%
Identity: 14%
PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus

Phyre2

PDB 1q57 chain G

3D model

Region: 2 - 128
Aligned: 75
Modelled: 75
Confidence: 93.4%
Identity: 24%
PDB header:transferase
Chain: G: PDB Molecule:dna primase/helicase;
PDBTitle: the crystal structure of the bifunctional primase-helicase of2 bacteriophage t7

Phyre2

PDB 3g3z chain A

3D model

Region: 493 - 577
Aligned: 77
Modelled: 85
Confidence: 92.9%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis

Phyre2
1

d1mw9x_
2

c2gajA_
3

c2o59B_
4

d1i7da_
5

c1gl9B_
6

d1gkub3
7

d1cy9a_
8

c1yuaA_
9

d1yuaa2
10

d1yuaa1
11

d1vdda_
12

c1vddC_
13

d2fcja1
14

c1i3qI_
15

d1nuia1
16

c3h0gI_
17

c1nuiA_
18

c2x4hA_
19

c1q57G_
20

c3g3zA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1mw9x_



100.0 98 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
2c2gajA_



100.0 38 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form
3c2o59B_



100.0 25 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
4d1i7da_



100.0 25 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
5c1gl9B_



100.0 28 PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp
6d1gkub3



100.0 28 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
7d1cy9a_



100.0 98 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
8c1yuaA_



100.0 99 PDB header:dna binding protein
Chain: A: PDB Molecule:topoisomerase i;
PDBTitle: c-terminal domain of escherichia coli topoisomerase i
9d1yuaa2



99.9 100 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Prokaryotic DNA topoisomerase I, a C-terminal fragment
10d1yuaa1



99.4 98 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Prokaryotic DNA topoisomerase I, a C-terminal fragment
11d1vdda_



99.2 25 Fold:Recombination protein RecR
Superfamily:Recombination protein RecR
Family:Recombination protein RecR
12c1vddC_



99.0 25 PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr
13d2fcja1



97.0 22 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
14c1i3qI_



96.5 13 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd
PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution
15d1nuia1



95.8 21 Fold:DNA primase core
Superfamily:DNA primase core
Family:Primase fragment of primase-helicase protein
16c3h0gI_



95.6 17 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
17c1nuiA_



95.2 21 PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein
18c2x4hA_



95.0 14 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
19c1q57G_



93.4 24 PDB header:transferase
Chain: G: PDB Molecule:dna primase/helicase;
PDBTitle: the crystal structure of the bifunctional primase-helicase of2 bacteriophage t7
20c3g3zA_



92.9 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
21c3hruA_



not modelled 92.0 8 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
22c1g3wA_



not modelled 90.9 9 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
23c1f5tA_



not modelled 90.5 9 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
24d2fxaa1



not modelled 90.5 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
25d2fbia1



not modelled 90.1 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
26c3nrvC_



not modelled 90.0 12 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
27d2fiya1



not modelled 89.9 18 Fold:FdhE-like
Superfamily:FdhE-like
Family:FdhE-like
28d1pvma3



not modelled 89.7 29 Fold:Rubredoxin-like
Superfamily:Hypothetical protein Ta0289 C-terminal domain
Family:Hypothetical protein Ta0289 C-terminal domain
29c2pexA_



not modelled 89.4 13 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator ohrr;
PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris
30c1fx7C_



not modelled 88.9 9 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
31c3s2wB_



not modelled 88.7 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
32d1t6t1_



not modelled 88.6 24 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
33d2a61a1



not modelled 88.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
34d1lnwa_



not modelled 88.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
35d1dgsa1



not modelled 88.1 36 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:NAD+-dependent DNA ligase, domain 3
36c3boqB_



not modelled 88.1 7 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcriptional regulator from2 silicibacter pomeroyi
37c3bjaA_



not modelled 87.6 17 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
38d1lj9a_



not modelled 87.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
39c3jw4C_



not modelled 87.2 13 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
40c2hr5B_



not modelled 87.2 25 PDB header:metal binding protein
Chain: B: PDB Molecule:rubrerythrin;
PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form
41c2gxgA_



not modelled 86.9 11 PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
42d1s3ja_



not modelled 86.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
43c3bj6B_



not modelled 86.8 14 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
44d3ctaa1



not modelled 86.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
45c2fxaB_



not modelled 86.4 27 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
46c2h09A_



not modelled 86.4 19 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
47c1v9pB_



not modelled 86.4 33 PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase
48c2f5qA_



not modelled 86.3 29 PDB header:hydrolase/dna
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase;
PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2
49c3kp3B_



not modelled 86.3 5 PDB header:transcription regulator/antibiotic
Chain: B: PDB Molecule:transcriptional regulator tcar;
PDBTitle: staphylococcus epidermidis in complex with ampicillin
50c2qwwB_



not modelled 86.1 17 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
51c3bpxB_



not modelled 86.0 16 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of marr
52c1dgsB_



not modelled 85.9 33 PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis
53c2opfA_



not modelled 85.4 19 PDB header:hydrolase/dna
Chain: A: PDB Molecule:endonuclease viii;
PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
54c2fa5B_



not modelled 85.3 16 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
55c2it0A_



not modelled 85.3 9 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
56d1twfi2



not modelled 85.2 14 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
57c1k82D_



not modelled 85.1 29 PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna
58c1nnjA_



not modelled 85.0 19 PDB header:hydrolase
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna
59c2rdpA_



not modelled 84.8 21 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
60d2hr3a1



not modelled 84.6 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
61d2bv6a1



not modelled 84.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
62d1p4xa1



not modelled 84.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
63c2nyxB_



not modelled 84.3 14 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
64c3floD_



not modelled 84.3 20 PDB header:transferase
Chain: D: PDB Molecule:dna polymerase alpha catalytic subunit a;
PDBTitle: crystal structure of the carboxyl-terminal domain of yeast2 dna polymerase alpha in complex with its b subunit
65d2fbha1



not modelled 84.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
66c1yuzB_



not modelled 84.2 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:nigerythrin;
PDBTitle: partially reduced state of nigerythrin
67c1ee8A_



not modelled 84.0 28 PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
68c3on1A_



not modelled 83.9 21 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:bh2414 protein;
PDBTitle: the structure of a protein with unknown function from bacillus2 halodurans c
69c3e6mD_



not modelled 83.6 13 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.
70c3f3xA_



not modelled 83.6 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
71d3broa1



not modelled 83.4 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
72d1r7ja_



not modelled 83.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Archaeal DNA-binding protein
73d1jgsa_



not modelled 83.1 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
74c3nqoB_



not modelled 83.1 13 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
75c3cdhB_



not modelled 82.6 24 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
76d2etha1



not modelled 82.2 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
77d1p4xa2



not modelled 81.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
78c2owoA_



not modelled 81.7 32 PDB header:ligase/dna
Chain: A: PDB Molecule:dna ligase;
PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate
79d1stza1



not modelled 81.0 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
80c3fm5D_



not modelled 80.5 19 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
81c3cjnA_



not modelled 79.9 25 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
82c2nnnB_



not modelled 79.4 13 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
83c3hrmA_



not modelled 79.4 14 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
84c3k0lA_



not modelled 79.3 11 PDB header:transcription regulator
Chain: A: PDB Molecule:repressor protein;
PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
85c1p4xA_



not modelled 78.8 13 PDB header:transcription
Chain: A: PDB Molecule:staphylococcal accessory regulator a homologue;
PDBTitle: crystal structure of sars protein from staphylococcus aureus
86d1ee8a3



not modelled 78.0 28 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
87d1ub9a_



not modelled 76.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
88d1tdza3



not modelled 76.6 19 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
89c3f2cA_



not modelled 76.5 31 PDB header:transferase/dna
Chain: A: PDB Molecule:geobacillus kaustophilus dna polc;
PDBTitle: dna polymerase polc from geobacillus kaustophilus complex with dna,2 dgtp and mn
90d1l1ta3



not modelled 76.0 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
91d1r2za3



not modelled 75.4 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
92d1k82a3



not modelled 74.9 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
93c3ecoB_



not modelled 74.7 10 PDB header:transcription
Chain: B: PDB Molecule:mepr;
PDBTitle: crystal structure of mepr, a transcription regulator of the2 staphylococcus aureus multidrug efflux pump mepa
94c2jrpA_



not modelled 73.9 21 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative cytoplasmic protein;
PDBTitle: solution nmr structure of yfgj from salmonella typhimurium2 modeled with two zn+2 bound, northeast structural genomics3 consortium target str86
95c2au3A_



not modelled 73.8 22 PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: crystal structure of the aquifex aeolicus primase (zinc binding and2 rna polymerase domains)
96c3oopA_



not modelled 73.3 18 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
97c3deuB_



not modelled 73.0 10 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
98d1k3xa3



not modelled 73.0 21 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
99d2fbka1



not modelled 72.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
100d3deua1



not modelled 72.6 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
101c3tgnA_



not modelled 72.4 11 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
102c3cngC_



not modelled 71.6 23 PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea
103c1dvbA_



not modelled 71.0 24 PDB header:electron transport
Chain: A: PDB Molecule:rubrerythrin;
PDBTitle: rubrerythrin
104c2ev5B_



not modelled 70.7 14 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
105c3nuhB_



not modelled 70.7 19 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
106c2wteB_



not modelled 70.5 15 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.
107d1olta_



not modelled 69.7 13 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:Oxygen-independent coproporphyrinogen III oxidase HemN
108c3ri2B_



not modelled 68.7 23 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
109c2hu9B_



not modelled 67.4 25 PDB header:metal transport
Chain: B: PDB Molecule:mercuric transport protein periplasmic component;
PDBTitle: x-ray structure of the archaeoglobus fulgidus copz n-2 terminal domain
110d1qypa_



not modelled 67.2 33 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
111d1z91a1



not modelled 66.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
112d2isya1



not modelled 65.8 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
113c3l09B_



not modelled 65.0 17 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
114c3ndjA_



not modelled 64.4 18 PDB header:transferase
Chain: A: PDB Molecule:methyltransferase;
PDBTitle: x-ray structure of a c-3'-methyltransferase in complex with s-2 adenosyl-l-homocysteine and sugar product
115c2jneA_



not modelled 63.6 16 PDB header:metal binding protein
Chain: A: PDB Molecule:hypothetical protein yfgj;
PDBTitle: nmr structure of e.coli yfgj modelled with two zn+2 bound.2 northeast structural genomics consortium target er317.
116d2jnea1



not modelled 63.6 16 Fold:Rubredoxin-like
Superfamily:YfgJ-like
Family:YfgJ-like
117c2k4bA_



not modelled 63.4 7 PDB header:dna binding protein
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: copr repressor structure
118d1g3wa1



not modelled 61.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
119d1jhfa1



not modelled 60.7 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
120d2p6ra1



not modelled 59.7 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:RecQ helicase DNA-binding 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