Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP33595
DateThu Jan 5 11:52:20 GMT 2012
Unique Job ID54852ff7525840dd

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3tpaA_
Top template information
PDB header:heme binding protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: structure of hbpa2 from haemophilus parasuis
Confidence and coverage
Confidence:100.0% Coverage: 78%
428 residues ( 78% 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.
547 residues ( 99%) 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  MPSARLQQQFIRLWQCCEGKSQDTTLNELAALLSCSRRHMRTLLNTMQDRGWLTWEAEVG
Secondary structure 
SS confidence 
Disorder  ???
?
???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  RGKRSRLTFLYTGLALQQQRAEDLLEQDRIDQLVQLVGDKATVRQMLVSHLGRSFRQGRH
Secondary structure 
SS confidence 
Disorder  ?
??
?????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  ILRVLYYRPLRNLLPGSALRRSETHIARQIFSSLTRINEENGELEADIAHHWQQISPLHW
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  RFFLRPGVHFHHGRELEMDDVIASLKRINTLPLYSHIADIVSPTPWTLDIHLTQPDRWLP
Secondary structure 
SS confidence 
Disorder 
?
??
??
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LLLGQVPAMILPREWETLSNFASHPIGTGPYAVIRNSTNQLKIQAFDDFFGYRALIDEVN
Secondary structure 
SS confidence 
Disorder 
???
????
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  VWVLPEIADEPAGGLMLKGPQGEEKEIESRLEEGCYYLLFDSRTHRGANQQVRDWVSYVL
Secondary structure 
SS confidence 
Disorder 
???
?????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  SPTNLVYFAEEQYQQLWFPAYGLLPRWHHARTIKSEKPAGLESLTLTFYQDHSEHRVIAG
Secondary structure 
SS confidence 
Disorder 
?
??????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  IMQQILASHQVTLKIKEIDYDQWHTGEIESDIWLNSANFTLPLDFSVFAHLCEVPLLQHC
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  IPIDWQADAARWRNGEMNLANWCQQLVASKAMVPLLHHWLIIQGQRSMRGLRMNTLGWFD
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........550.
Sequence  FKSAWFAPPDP
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 3tpa chain A

3D model

Region: 120 - 547
Aligned: 428
Modelled: 428
Confidence: 100.0%
Identity: 17%
PDB header:heme binding protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: structure of hbpa2 from haemophilus parasuis

Phyre2

PDB 1dpe chain A

3D model

Region: 120 - 547
Aligned: 428
Modelled: 428
Confidence: 100.0%
Identity: 18%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 2wok chain A

3D model

Region: 121 - 547
Aligned: 426
Modelled: 427
Confidence: 100.0%
Identity: 18%
PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:clavulanic acid biosynthesis oligopeptide
PDBTitle: clavulanic acid biosynthesis oligopeptide2 binding protein 2 complexed with bradykinin

Phyre2

PDB 1jet chain A

3D model

Region: 112 - 549
Aligned: 433
Modelled: 435
Confidence: 100.0%
Identity: 15%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3m8u chain A

3D model

Region: 119 - 547
Aligned: 429
Modelled: 429
Confidence: 100.0%
Identity: 16%
PDB header:transport protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: crystal structure of glutathione-binding protein a (gbpa) from2 haemophilus parasuis sh0165 in complex with glutathione disulfide3 (gssg)

Phyre2

PDB 1uqw chain A

3D model

Region: 120 - 547
Aligned: 427
Modelled: 421
Confidence: 100.0%
Identity: 19%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3o9p chain A

3D model

Region: 114 - 549
Aligned: 432
Modelled: 433
Confidence: 100.0%
Identity: 16%
PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:periplasmic murein peptide-binding protein;
PDBTitle: the structure of the escherichia coli murein tripeptide binding2 protein mppa

Phyre2

PDB 1zlq chain A domain 1

3D model

Region: 120 - 544
Aligned: 423
Modelled: 425
Confidence: 100.0%
Identity: 14%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 1xoc chain A domain 1

3D model

Region: 121 - 547
Aligned: 422
Modelled: 427
Confidence: 100.0%
Identity: 19%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3t66 chain A

3D model

Region: 119 - 546
Aligned: 422
Modelled: 428
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:nickel abc transporter (nickel-binding protein);
PDBTitle: crystal structure of nickel abc transporter from bacillus halodurans

Phyre2

PDB 3rqt chain A

3D model

Region: 121 - 549
Aligned: 420
Modelled: 423
Confidence: 100.0%
Identity: 13%
PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: 1.5 angstrom crystal structure of the complex of ligand binding2 component of abc-type import system from staphylococcus aureus with3 nickel and two histidines

Phyre2

PDB 3ry3 chain B

3D model

Region: 121 - 545
Aligned: 415
Modelled: 422
Confidence: 100.0%
Identity: 16%
PDB header:transport protein
Chain: B: PDB Molecule:putative solute-binding protein;
PDBTitle: putative solute-binding protein from yersinia pestis.

Phyre2

PDB 1vr5 chain A domain 1

3D model

Region: 117 - 545
Aligned: 427
Modelled: 429
Confidence: 100.0%
Identity: 15%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 2o7j chain A

3D model

Region: 119 - 551
Aligned: 431
Modelled: 433
Confidence: 100.0%
Identity: 13%
PDB header:sugar binding protein
Chain: A: PDB Molecule:oligopeptide abc transporter, periplasmic
PDBTitle: the x-ray crystal structure of a thermophilic cellobiose2 binding protein bound with cellopentaose

Phyre2

PDB 2grv chain C

3D model

Region: 121 - 535
Aligned: 414
Modelled: 415
Confidence: 100.0%
Identity: 13%
PDB header:biosynthetic protein
Chain: C: PDB Molecule:lpqw;
PDBTitle: crystal structure of lpqw

Phyre2

PDB 3fto chain A

3D model

Region: 121 - 549
Aligned: 424
Modelled: 424
Confidence: 100.0%
Identity: 13%
PDB header:peptide binding protein
Chain: A: PDB Molecule:oligopeptide-binding protein oppa;
PDBTitle: crystal structure of oppa in a open conformation

Phyre2

PDB 1zty chain A

3D model

Region: 119 - 541
Aligned: 419
Modelled: 423
Confidence: 100.0%
Identity: 15%
PDB header:sugar binding protein, signaling protein
Chain: A: PDB Molecule:chitin oligosaccharide binding protein;
PDBTitle: crystal structure of the chitin oligasaccharide binding2 protein

Phyre2

PDB 2d5w chain A

3D model

Region: 120 - 547
Aligned: 424
Modelled: 428
Confidence: 100.0%
Identity: 13%
PDB header:peptide binding protein
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: the crystal structure of oligopeptide binding protein from thermus2 thermophilus hb8 complexed with pentapeptide

Phyre2

PDB 3pam chain B

3D model

Region: 335 - 517
Aligned: 180
Modelled: 181
Confidence: 99.8%
Identity: 16%
PDB header:transport protein
Chain: B: PDB Molecule:transmembrane protein;
PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1

Phyre2

PDB 3lvu chain B

3D model

Region: 332 - 517
Aligned: 186
Modelled: 186
Confidence: 99.8%
Identity: 15%
PDB header:transport protein
Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding protein;
PDBTitle: crystal structure of abc transporter, periplasmic substrate-binding2 protein spo2066 from silicibacter pomeroyi

Phyre2

PDB 1lnw chain A

3D model

Region: 7 - 111
Aligned: 101
Modelled: 99
Confidence: 97.3%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2

PDB 1i5z chain A domain 1

3D model

Region: 5 - 59
Aligned: 55
Modelled: 55
Confidence: 97.1%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: CAP C-terminal domain-like

Phyre2

PDB 1sfx chain A

3D model

Region: 9 - 100
Aligned: 87
Modelled: 85
Confidence: 97.1%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: TrmB-like

Phyre2

PDB 2oz6 chain A domain 1

3D model

Region: 3 - 59
Aligned: 57
Modelled: 57
Confidence: 97.1%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: CAP C-terminal domain-like

Phyre2

PDB 3g3z chain A

3D model

Region: 7 - 111
Aligned: 100
Modelled: 99
Confidence: 97.0%
Identity: 11%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis

Phyre2

PDB 3bj6 chain B

3D model

Region: 9 - 113
Aligned: 101
Modelled: 99
Confidence: 97.0%
Identity: 13%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579

Phyre2

PDB 3bro chain A domain 1

3D model

Region: 8 - 111
Aligned: 102
Modelled: 96
Confidence: 96.7%
Identity: 12%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
1
c3tpaA_
2
d1dpea_
3
c2wokA_
4
d1jeta_
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c3m8uA_
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d1uqwa_
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c3o9pA_
8
d1zlqa1
9
d1xoca1
10
c3t66A_
11
c3rqtA_
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c3ry3B_
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d1vr5a1
14
c2o7jA_
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c2grvC_
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c3ftoA_
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c1ztyA_
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c2d5wA_
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c3pamB_
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c3lvuB_
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d1lnwa_
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d1i5za1
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d1sfxa_
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d2oz6a1
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c3g3zA_
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c3bj6B_
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d3broa1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3tpaA_
100.0 17 PDB header:heme binding protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: structure of hbpa2 from haemophilus parasuis
2d1dpea_
100.0 18 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
3c2wokA_
100.0 18 PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:clavulanic acid biosynthesis oligopeptide
PDBTitle: clavulanic acid biosynthesis oligopeptide2 binding protein 2 complexed with bradykinin
4d1jeta_
100.0 15 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
5c3m8uA_
100.0 16 PDB header:transport protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: crystal structure of glutathione-binding protein a (gbpa) from2 haemophilus parasuis sh0165 in complex with glutathione disulfide3 (gssg)
6d1uqwa_
100.0 19 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
7c3o9pA_
100.0 16 PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:periplasmic murein peptide-binding protein;
PDBTitle: the structure of the escherichia coli murein tripeptide binding2 protein mppa
8d1zlqa1
100.0 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
9d1xoca1
100.0 19 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
10c3t66A_
100.0 18 PDB header:transport protein
Chain: A: PDB Molecule:nickel abc transporter (nickel-binding protein);
PDBTitle: crystal structure of nickel abc transporter from bacillus halodurans
11c3rqtA_
100.0 13 PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: 1.5 angstrom crystal structure of the complex of ligand binding2 component of abc-type import system from staphylococcus aureus with3 nickel and two histidines
12c3ry3B_
100.0 16 PDB header:transport protein
Chain: B: PDB Molecule:putative solute-binding protein;
PDBTitle: putative solute-binding protein from yersinia pestis.
13d1vr5a1
100.0 15 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
14c2o7jA_
100.0 13 PDB header:sugar binding protein
Chain: A: PDB Molecule:oligopeptide abc transporter, periplasmic
PDBTitle: the x-ray crystal structure of a thermophilic cellobiose2 binding protein bound with cellopentaose
15c2grvC_
100.0 13 PDB header:biosynthetic protein
Chain: C: PDB Molecule:lpqw;
PDBTitle: crystal structure of lpqw
16c3ftoA_
100.0 13 PDB header:peptide binding protein
Chain: A: PDB Molecule:oligopeptide-binding protein oppa;
PDBTitle: crystal structure of oppa in a open conformation
17c1ztyA_
100.0 15 PDB header:sugar binding protein, signaling protein
Chain: A: PDB Molecule:chitin oligosaccharide binding protein;
PDBTitle: crystal structure of the chitin oligasaccharide binding2 protein
18c2d5wA_
100.0 13 PDB header:peptide binding protein
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: the crystal structure of oligopeptide binding protein from thermus2 thermophilus hb8 complexed with pentapeptide
19c3pamB_
99.8 16 PDB header:transport protein
Chain: B: PDB Molecule:transmembrane protein;
PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1
20c3lvuB_
99.8 15 PDB header:transport protein
Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding protein;
PDBTitle: crystal structure of abc transporter, periplasmic substrate-binding2 protein spo2066 from silicibacter pomeroyi
21c3o6pA_
not modelled 99.7 16 PDB header:protein binding
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: crystal structure of peptide abc transporter, peptide-binding protein
22d1lnwa_
97.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
23d1i5za1
97.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
24d1sfxa_
97.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
25d2oz6a1
97.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
26c3g3zA_
97.0 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
27c3bj6B_
97.0 13 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
28d2h6ca1
not modelled 96.9 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
29d2gaua1
not modelled 96.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
30d1biaa1
not modelled 96.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
31c3nqoB_
not modelled 96.8 11 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
32d1hsja1
not modelled 96.8 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
33c2gxgA_
not modelled 96.7 10 PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
34d2fbha1
not modelled 96.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
35d2etha1
not modelled 96.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
36d1lj9a_
not modelled 96.7 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
37d3broa1
96.7 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
38d1s3ja_
not modelled 96.6 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
39c3fm5D_
not modelled 96.6 13 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
40d1ft9a1
not modelled 96.6 32 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
41d1p4xa1
not modelled 96.6 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
42c1ft9A_
not modelled 96.6 28 PDB header:transcription
Chain: A: PDB Molecule:carbon monoxide oxidation system transcription
PDBTitle: structure of the reduced (feii) co-sensing protein from r.2 rubrum
43c3r0aB_
not modelled 96.6 5 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
44c3dv8A_
not modelled 96.5 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of a putative transcriptional regulator of the2 crp/fnr family (eubrec_1222) from eubacterium rectale atcc 33656 at3 2.55 a resolution
45c3ctaA_
not modelled 96.5 18 PDB header:transferase
Chain: A: PDB Molecule:riboflavin kinase;
PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
46d2coha1
not modelled 96.5 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
47c3bjaA_
not modelled 96.4 12 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
48c2v79B_
not modelled 96.4 19 PDB header:dna-binding protein
Chain: B: PDB Molecule:dna replication protein dnad;
PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis
49c1fx7C_
not modelled 96.3 15 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
50c3hrmA_
not modelled 96.3 12 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
51d2frha1
not modelled 96.3 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
52c3f3xA_
not modelled 96.3 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
53d1p4xa2
not modelled 96.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
54d1j5ya1
not modelled 96.2 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
55c3e6mD_
not modelled 96.2 14 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.
56d2a61a1
not modelled 96.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
57d3ctaa1
not modelled 96.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
58c2oz6A_
not modelled 96.0 18 PDB header:dna binding protein
Chain: A: PDB Molecule:virulence factor regulator;
PDBTitle: crystal structure of virulence factor regulator from pseudomonas2 aeruginosa in complex with camp
59c2nnnB_
not modelled 96.0 18 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
60c3cjnA_
not modelled 96.0 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
61c2gauA_
not modelled 95.9 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator, crp/fnr family from2 porphyromonas gingivalis (apc80792), structural genomics, mcsg
62c3k0lA_
not modelled 95.9 18 PDB header:transcription regulator
Chain: A: PDB Molecule:repressor protein;
PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
63d1jgsa_
not modelled 95.8 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
64c3iwzB_
not modelled 95.8 27 PDB header:transcription
Chain: B: PDB Molecule:catabolite activation-like protein;
PDBTitle: the c-di-gmp responsive global regulator clp links cell-cell signaling2 to virulence gene expression in xanthomonas campestris
65c1p4xA_
not modelled 95.8 6 PDB header:transcription
Chain: A: PDB Molecule:staphylococcal accessory regulator a homologue;
PDBTitle: crystal structure of sars protein from staphylococcus aureus
66d1jhfa1
not modelled 95.7 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
67d3e5ua1
not modelled 95.7 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
68d2fbia1
not modelled 95.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
69c3neuA_
not modelled 95.7 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
70c3e6dA_
not modelled 95.7 5 PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s
71c2x4hA_
not modelled 95.6 11 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
72c2rdpA_
not modelled 95.5 13 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
73d2bgca1
not modelled 95.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
74c3by6C_
not modelled 95.4 11 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
75c2fxaB_
not modelled 95.4 12 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
76c1zybA_
not modelled 95.4 26 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator, crp family;
PDBTitle: crystal structure of transcription regulator from bacteroides2 thetaiotaomicron vpi-5482 at 2.15 a resolution
77d1ub9a_
not modelled 95.4 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
78c2zdbA_
not modelled 95.4 13 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp family;
PDBTitle: crystal structure of tthb099, a transcriptional regulator crp family2 from thermus thermophilus hb8
79c3bpxB_
not modelled 95.3 13 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of marr
80c1g3wA_
not modelled 95.3 11 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
81c3d0sA_
not modelled 95.2 29 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form
82c2it0A_
not modelled 95.2 12 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
83c2fa5B_
not modelled 95.2 8 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
84d2isya1
not modelled 95.2 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
85d2bv6a1
not modelled 95.2 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
86c2nyxB_
not modelled 95.2 13 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
87c3kccA_
not modelled 95.0 22 PDB header:transcription
Chain: A: PDB Molecule:catabolite gene activator;
PDBTitle: crystal structure of d138l mutant of catabolite gene activator protein
88c1f5tA_
not modelled 95.0 11 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
89d2hr3a1
not modelled 95.0 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
90c2zcwA_
not modelled 94.9 18 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, fnr/crp family;
PDBTitle: crystal structure of ttha1359, a transcriptional regulator,2 crp/fnr family from thermus thermophilus hb8
91c3hruA_
not modelled 94.9 15 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
92d1mkma1
not modelled 94.8 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
93d1g3wa1
not modelled 94.8 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
94c2y75F_
not modelled 94.7 15 PDB header:transcription
Chain: F: PDB Molecule:hth-type transcriptional regulator cymr;
PDBTitle: the structure of cymr (yrzc) the global cysteine regulator2 of b. subtilis
95c3e97A_
not modelled 94.6 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator of crp/fnr2 family (yp_604437.1) from deinococcus geothermalis dsm3 11300 at 1.86 a resolution
96d1stza1
not modelled 94.6 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
97c3s2wB_
not modelled 94.5 17 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
98d2fbka1
not modelled 94.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
99c3dkwB_
not modelled 94.4 15 PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.
100d1zyba1
not modelled 94.4 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
101d1u2wa1
not modelled 94.4 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
102c2bgcA_
not modelled 94.4 13 PDB header:transcription
Chain: A: PDB Molecule:prfa;
PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes
103c2vn2B_
not modelled 94.3 16 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
104d1ku9a_
not modelled 94.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
105c2qwwB_
not modelled 94.2 8 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
106c3deuB_
not modelled 94.2 16 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
107c1zreB_
not modelled 94.2 18 PDB header:gene regulation/dna
Chain: B: PDB Molecule:catabolite gene activator;
PDBTitle: 4 crystal structures of cap-dna with all base-pair2 substitutions at position 6, cap-[6g;17c]icap38 dna
108d2ev0a1
not modelled 94.1 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
109c3oopA_
not modelled 94.1 11 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
110c2fmyB_
not modelled 94.1 23 PDB header:dna binding protein
Chain: B: PDB Molecule:carbon monoxide oxidation system transcription regulator
PDBTitle: co-dependent transcription factor cooa from carboxydothermus2 hydrogenoformans (imidazole-bound form)
111c2o0yB_
not modelled 94.1 22 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator rha1_ro069532 (iclr-family) from rhodococcus sp.
112c3nrvC_
not modelled 94.0 6 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
113d1z91a1
not modelled 94.0 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
114d1z05a1
not modelled 93.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
115c3la2A_
not modelled 93.9 13 PDB header:transcription
Chain: A: PDB Molecule:global nitrogen regulator;
PDBTitle: crystal structure of ntca in complex with 2-oxoglutarate
116c2h09A_
not modelled 93.8 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
117c3kp3B_
not modelled 93.8 9 PDB header:transcription regulator/antibiotic
Chain: B: PDB Molecule:transcriptional regulator tcar;
PDBTitle: staphylococcus epidermidis in complex with ampicillin
118c1mkmA_
not modelled 93.5 12 PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr
119d3deua1
not modelled 93.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
120d3bwga1
not modelled 93.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators

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