Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP46890
DateThu Jan 5 12:04:38 GMT 2012
Unique Job ID029d1fe068e8f597

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%
442 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.
559 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  MRLLNRLNQYQRLWQPSAGKPQTVTVSELAERCFCSERHVRTLLRQAQEAGWLEWQAQSG
Secondary structure 
SS confidence 
Disorder  ???
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  RGKRGQLRFLVTPESLRNAMMEQALETGKQQDVLELAQLAPGELRTLLQPFMGGQWQNDT
Secondary structure 
SS confidence 
Disorder  ?
?
?????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  PTLRIPYYRPLEPLQPGFLPGRAEQHLAGQIFSGLTRFDNNTQRPIGDLAHHWETSTDGL
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  RWDFYLRSTLHWHNGDAVKASHLHQRLLMLLQLPALDQLFISVKRIEVTHPQCLTFFLHR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  PDYWLAHRLASYCSHLAHPQFPLIGTGPFRLTQFTAELVRLESHDYYHLRHPLLKAVEYW
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  ITPPLFEKDLGTSCRHPVQITIGKPEELQRVSQVSSGISLGFCYLTLRKSPRLSLWQARK
Secondary structure 
SS confidence 
Disorder 
??
?
????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  VISIIHQSGLLQTLEVGENLITASHALLPGWTIPHWQVPDEVKLPKTLTLVYHLPIELHT
Secondary structure 
SS confidence 
Disorder 
?????
?
??
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  MAERLQATLAAEGCELTIIFHNAKNWDDTTLQAHADLMMGDRLIGEAPEYTLEQWLRCDP
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  LWPHVFDAPAYAHLQSTLDAVQIMPDEENRFNALKAVFSQLMTDATLTPLFNYHYRISAP
Secondary structure 
SS confidence 
Disorder 
?
?
?
Disorder confidence 
 
   .........550.........560......
Sequence  PGVNGVRLTPRGWFEFTEAWLPAPSQ
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: 121 - 562
Aligned: 442
Modelled: 442
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: 121 - 562
Aligned: 442
Modelled: 442
Confidence: 100.0%
Identity: 17%
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: 122 - 563
Aligned: 442
Modelled: 442
Confidence: 100.0%
Identity: 19%
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 3m8u chain A

3D model

Region: 121 - 562
Aligned: 442
Modelled: 442
Confidence: 100.0%
Identity: 15%
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 3o9p chain A

3D model

Region: 119 - 563
Aligned: 439
Modelled: 445
Confidence: 100.0%
Identity: 15%
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 1uqw chain A

3D model

Region: 119 - 562
Aligned: 443
Modelled: 444
Confidence: 100.0%
Identity: 15%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 1jet chain A

3D model

Region: 119 - 563
Aligned: 439
Modelled: 445
Confidence: 100.0%
Identity: 16%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 1zlq chain A domain 1

3D model

Region: 121 - 559
Aligned: 437
Modelled: 439
Confidence: 100.0%
Identity: 16%
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 - 563
Aligned: 438
Modelled: 442
Confidence: 100.0%
Identity: 14%
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: 120 - 561
Aligned: 437
Modelled: 442
Confidence: 100.0%
Identity: 15%
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: 122 - 557
Aligned: 425
Modelled: 432
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 1vr5 chain A domain 1

3D model

Region: 121 - 560
Aligned: 437
Modelled: 440
Confidence: 100.0%
Identity: 14%
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: 120 - 563
Aligned: 435
Modelled: 439
Confidence: 100.0%
Identity: 14%
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 1zty chain A

3D model

Region: 120 - 556
Aligned: 435
Modelled: 432
Confidence: 100.0%
Identity: 13%
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 3fto chain A

3D model

Region: 122 - 565
Aligned: 436
Modelled: 442
Confidence: 100.0%
Identity: 14%
PDB header:peptide binding protein
Chain: A: PDB Molecule:oligopeptide-binding protein oppa;
PDBTitle: crystal structure of oppa in a open conformation

Phyre2

PDB 3ry3 chain B

3D model

Region: 122 - 560
Aligned: 428
Modelled: 436
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 2grv chain C

3D model

Region: 122 - 551
Aligned: 428
Modelled: 429
Confidence: 100.0%
Identity: 13%
PDB header:biosynthetic protein
Chain: C: PDB Molecule:lpqw;
PDBTitle: crystal structure of lpqw

Phyre2

PDB 2d5w chain A

3D model

Region: 121 - 560
Aligned: 436
Modelled: 440
Confidence: 100.0%
Identity: 11%
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 3lvu chain B

3D model

Region: 339 - 532
Aligned: 194
Modelled: 192
Confidence: 99.9%
Identity: 13%
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 3pam chain B

3D model

Region: 339 - 532
Aligned: 192
Modelled: 194
Confidence: 99.9%
Identity: 14%
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 1i5z chain A domain 1

3D model

Region: 5 - 59
Aligned: 55
Modelled: 55
Confidence: 97.1%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: CAP C-terminal domain-like

Phyre2

PDB 1lnw chain A

3D model

Region: 7 - 112
Aligned: 102
Modelled: 100
Confidence: 97.1%
Identity: 8%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2

PDB 2oz6 chain A domain 1

3D model

Region: 5 - 58
Aligned: 54
Modelled: 54
Confidence: 97.1%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: CAP C-terminal domain-like

Phyre2

PDB 1bia chain A domain 1

3D model

Region: 1 - 60
Aligned: 56
Modelled: 56
Confidence: 96.9%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2

PDB 1sfx chain A

3D model

Region: 23 - 87
Aligned: 64
Modelled: 63
Confidence: 96.8%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: TrmB-like

Phyre2

PDB 3dv8 chain A

3D model

Region: 4 - 82
Aligned: 70
Modelled: 69
Confidence: 96.6%
Identity: 13%
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

Phyre2

PDB 3g3z chain A

3D model

Region: 7 - 110
Aligned: 102
Modelled: 101
Confidence: 96.5%
Identity: 13%
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 3e6m chain D

3D model

Region: 23 - 112
Aligned: 89
Modelled: 88
Confidence: 95.7%
Identity: 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.

Phyre2

PDB 2fbk chain A domain 1

3D model

Region: 3 - 114
Aligned: 102
Modelled: 102
Confidence: 94.4%
Identity: 17%
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
c3m8uA_
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c3o9pA_
6
d1uqwa_
7
d1jeta_
8
d1zlqa1
9
d1xoca1
10
c3t66A_
11
c3rqtA_
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d1vr5a1
13
c2o7jA_
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c1ztyA_
15
c3ftoA_
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c3ry3B_
17
c2grvC_
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c2d5wA_
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c3lvuB_
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c3pamB_
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d1i5za1
23
d1lnwa_
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d2oz6a1
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d1biaa1
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d1sfxa_
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c3dv8A_
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c3g3zA_
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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 17 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
3c2wokA_
100.0 19 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
4c3m8uA_
100.0 15 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)
5c3o9pA_
100.0 15 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
6d1uqwa_
100.0 15 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
7d1jeta_
100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
8d1zlqa1
100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
9d1xoca1
100.0 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
10c3t66A_
100.0 15 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
12d1vr5a1
100.0 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
13c2o7jA_
100.0 14 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
14c1ztyA_
100.0 13 PDB header:sugar binding protein, signaling protein
Chain: A: PDB Molecule:chitin oligosaccharide binding protein;
PDBTitle: crystal structure of the chitin oligasaccharide binding2 protein
15c3ftoA_
100.0 14 PDB header:peptide binding protein
Chain: A: PDB Molecule:oligopeptide-binding protein oppa;
PDBTitle: crystal structure of oppa in a open conformation
16c3ry3B_
100.0 16 PDB header:transport protein
Chain: B: PDB Molecule:putative solute-binding protein;
PDBTitle: putative solute-binding protein from yersinia pestis.
17c2grvC_
100.0 13 PDB header:biosynthetic protein
Chain: C: PDB Molecule:lpqw;
PDBTitle: crystal structure of lpqw
18c2d5wA_
100.0 11 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
19c3lvuB_
99.9 13 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
20c3pamB_
99.9 14 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
21c3o6pA_
not modelled 99.8 17 PDB header:protein binding
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: crystal structure of peptide abc transporter, peptide-binding protein
22d1i5za1
97.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
23d1lnwa_
97.1 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
24d2oz6a1
97.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
25d1biaa1
96.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
26d1sfxa_
96.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
27d2h6ca1
not modelled 96.8 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
28d2gaua1
not modelled 96.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
29c3bj6B_
not modelled 96.7 11 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
30c3dv8A_
96.6 13 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
31c3fm5D_
not modelled 96.6 11 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
32c3g3zA_
96.5 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
33d1hsja1
not modelled 96.5 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
34d2coha1
not modelled 96.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
35d1lj9a_
not modelled 96.4 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
36c1ft9A_
not modelled 96.4 23 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
37c3hrmA_
not modelled 96.3 15 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
38d1ft9a1
not modelled 96.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
39d1p4xa1
not modelled 96.3 3 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
40c2gxgA_
not modelled 96.3 17 PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
41c3ctaA_
not modelled 96.2 12 PDB header:transferase
Chain: A: PDB Molecule:riboflavin kinase;
PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
42d3broa1
not modelled 96.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
43d2frha1
not modelled 96.2 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
44d2etha1
not modelled 96.2 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
45d2fbha1
not modelled 96.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
46c3r0aB_
not modelled 96.1 8 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
47d1j5ya1
not modelled 96.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
48c2v79B_
not modelled 96.1 15 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
49d1p4xa2
not modelled 96.1 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
50c3nqoB_
not modelled 96.1 9 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
51c3by6C_
not modelled 96.1 11 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
52d3ctaa1
not modelled 96.0 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
53c2oz6A_
not modelled 96.0 17 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
54d1s3ja_
not modelled 96.0 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
55c2gauA_
not modelled 95.9 14 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
56c3neuA_
not modelled 95.7 16 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
57c3d0sA_
not modelled 95.7 21 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form
58c3e6mD_
95.7 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.
59c3e6dA_
not modelled 95.7 7 PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s
60c3iwzB_
not modelled 95.6 22 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
61c2x4hA_
not modelled 95.5 10 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
62c1p4xA_
not modelled 95.5 3 PDB header:transcription
Chain: A: PDB Molecule:staphylococcal accessory regulator a homologue;
PDBTitle: crystal structure of sars protein from staphylococcus aureus
63d3e5ua1
not modelled 95.4 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
64c2y75F_
not modelled 95.4 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
65c2nyxB_
not modelled 95.4 14 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
66c3e97A_
not modelled 95.4 14 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
67c2zdbA_
not modelled 95.3 18 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
68c1zybA_
not modelled 95.3 15 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
69d2bgca1
not modelled 95.2 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
70c2bgcA_
not modelled 95.1 11 PDB header:transcription
Chain: A: PDB Molecule:prfa;
PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes
71c3kccA_
not modelled 95.1 13 PDB header:transcription
Chain: A: PDB Molecule:catabolite gene activator;
PDBTitle: crystal structure of d138l mutant of catabolite gene activator protein
72c3l6gA_
not modelled 95.1 18 PDB header:glycine betaine-binding protein
Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding
PDBTitle: crystal structure of lactococcal opuac in its open conformation
73d1zyba1
not modelled 95.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
74c2rdpA_
not modelled 95.0 11 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
75d1ub9a_
not modelled 95.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
76c3chgB_
not modelled 94.9 16 PDB header:ligand binding protein
Chain: B: PDB Molecule:glycine betaine-binding protein;
PDBTitle: the compatible solute-binding protein opuac from bacillus2 subtilis in complex with dmsa
77c3bjaA_
not modelled 94.9 14 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
78c2zcwA_
not modelled 94.8 16 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
79d1z05a1
not modelled 94.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
80d2a61a1
not modelled 94.8 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
81d1mkma1
not modelled 94.7 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
82d1jhfa1
not modelled 94.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
83c1fx7C_
not modelled 94.6 18 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
84c2it0A_
not modelled 94.6 19 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
85c3f3xA_
not modelled 94.6 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
86c1g3wA_
not modelled 94.6 17 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
87c2fmyB_
not modelled 94.5 18 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)
88c3dkwB_
not modelled 94.5 9 PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.
89c2fxaB_
not modelled 94.5 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.
90d2isya1
not modelled 94.5 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
91c3bpxB_
not modelled 94.5 15 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of marr
92d2fbka1
94.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
93c3tmgA_
not modelled 94.4 10 PDB header:transport protein
Chain: A: PDB Molecule:glycine betaine, l-proline abc transporter,
PDBTitle: crystal structure of glycine betaine, l-proline abc transporter,2 glycine/betaine/l-proline-binding protein (prox) from borrelia3 burgdorferi
94c3cjnA_
not modelled 94.4 10 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
95c3hruA_
not modelled 94.3 18 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
96d2bv6a1
not modelled 94.3 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
97c3s2wB_
not modelled 94.3 10 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
98c1f5tA_
not modelled 94.2 17 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
99c2nnnB_
not modelled 94.1 13 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
100c1zreB_
not modelled 94.1 13 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
101c3la2A_
not modelled 94.0 19 PDB header:transcription
Chain: A: PDB Molecule:global nitrogen regulator;
PDBTitle: crystal structure of ntca in complex with 2-oxoglutarate
102d1jgsa_
not modelled 93.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
103c2du9A_
not modelled 93.8 22 PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
104d2fbia1
not modelled 93.7 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
105c3lwfD_
not modelled 93.7 19 PDB header:transcription regulator
Chain: D: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator (np_470886.1)2 from listeria innocua at 2.06 a resolution
106d1g3wa1
not modelled 93.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
107c3fx3A_
not modelled 93.5 13 PDB header:camp-binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: structure of a putative camp-binding regulatory protein from2 silicibacter pomeroyi dss-3
108c2fa5B_
not modelled 93.5 11 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
109d1stza1
not modelled 93.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
110c1mkmA_
not modelled 93.3 23 PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr
111c2vn2B_
not modelled 93.2 20 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
112c2h09A_
not modelled 93.1 17 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
113c3k0lA_
not modelled 93.1 21 PDB header:transcription regulator
Chain: A: PDB Molecule:repressor protein;
PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
114c2pexA_
not modelled 93.0 25 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator ohrr;
PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris
115c3deuB_
not modelled 93.0 15 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
116d3deua1
not modelled 92.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
117c3ecoB_
not modelled 92.9 15 PDB header:transcription
Chain: B: PDB Molecule:mepr;
PDBTitle: crystal structure of mepr, a transcription regulator of the2 staphylococcus aureus multidrug efflux pump mepa
118c3nrvC_
not modelled 92.8 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
119c2qwwB_
not modelled 92.8 14 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
120d2hs5a1
not modelled 92.7 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
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Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0