Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ47129
DateThu Jan 5 12:36:13 GMT 2012
Unique Job ID68b0784d440c2b6e

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3gbgA_
Top template information
PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395
Confidence and coverage
Confidence:100.0% Coverage: 77%
232 residues ( 77% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MNPAVDNEFQQWLSQINQVCGNFTGRLLTERYTGVLDTHFAKGLKLSTVTTSGVNLSRTW
Secondary structure 
SS confidence 
Disorder  ????
????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  QEVKGSDDAWFYTVFQLSGQAIMEQDERQVQIGAGDITLLDASRPCSLYWQESSKQISLL
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  LPRTLLEQYFPHQKPICAERLDADLPMVQLSHRLLQESMNNPALSETESEAALQAMVCLL
Secondary structure 
SS confidence 
Disorder 
?
????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  RPVLHQRESVQPRRERQFQKVVTLIDDNIREEILRPEWIAGETGMSVRSLYRMFADKGLV
Secondary structure 
SS confidence 
Disorder 
???????????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  VAQYIRNRRLDFCADAIRHAADDEKLAGIGFHWGFSDQSHFSTVFKQRFGMTPGEYRRKF
Secondary structure 
SS confidence 
Disorder 
??????
??
Disorder confidence 
 
   .
Sequence  R
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 3gbg chain A

3D model

Region: 63 - 299
Aligned: 232
Modelled: 237
Confidence: 100.0%
Identity: 15%
PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395

Phyre2

PDB 1d5y chain D

3D model

Region: 194 - 301
Aligned: 105
Modelled: 108
Confidence: 99.9%
Identity: 30%
PDB header:transcription/dna
Chain: D: PDB Molecule:rob transcription factor;
PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna

Phyre2

PDB 2k9s chain A

3D model

Region: 195 - 300
Aligned: 104
Modelled: 106
Confidence: 99.9%
Identity: 23%
PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac

Phyre2

PDB 3mn2 chain B

3D model

Region: 196 - 301
Aligned: 105
Modelled: 106
Confidence: 99.9%
Identity: 22%
PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009

Phyre2

PDB 3oio chain A

3D model

Region: 191 - 301
Aligned: 108
Modelled: 111
Confidence: 99.9%
Identity: 31%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum

Phyre2

PDB 3oou chain A

3D model

Region: 197 - 301
Aligned: 102
Modelled: 105
Confidence: 99.9%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua

Phyre2

PDB 3mkl chain B

3D model

Region: 191 - 301
Aligned: 108
Modelled: 111
Confidence: 99.9%
Identity: 21%
PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12

Phyre2

PDB 1bl0 chain A

3D model

Region: 194 - 301
Aligned: 105
Modelled: 108
Confidence: 99.9%
Identity: 28%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex

Phyre2

PDB 3lsg chain D

3D model

Region: 199 - 289
Aligned: 89
Modelled: 91
Confidence: 99.8%
Identity: 18%
PDB header:transcription regulator
Chain: D: PDB Molecule:two-component response regulator yesn;
PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586

Phyre2

PDB 1bl0 chain A domain 2

3D model

Region: 249 - 301
Aligned: 51
Modelled: 53
Confidence: 99.4%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1d5y chain A domain 2

3D model

Region: 249 - 301
Aligned: 51
Modelled: 53
Confidence: 99.4%
Identity: 33%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1zgw chain A

3D model

Region: 172 - 252
Aligned: 81
Modelled: 81
Confidence: 98.8%
Identity: 20%
PDB header:transcription regulator/dna
Chain: A: PDB Molecule:ada polyprotein;
PDBTitle: nmr structure of e. coli ada protein in complex with dna

Phyre2

PDB 1d5y chain A domain 1

3D model

Region: 194 - 246
Aligned: 52
Modelled: 53
Confidence: 98.7%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1bl0 chain A domain 1

3D model

Region: 194 - 246
Aligned: 52
Modelled: 53
Confidence: 98.7%
Identity: 33%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 2arc chain A

3D model

Region: 64 - 184
Aligned: 121
Modelled: 121
Confidence: 98.7%
Identity: 10%
Fold: Double-stranded beta-helix
Superfamily: Regulatory protein AraC
Family: Regulatory protein AraC

Phyre2

PDB 2pfw chain B

3D model

Region: 34 - 123
Aligned: 84
Modelled: 90
Confidence: 98.0%
Identity: 11%
PDB header:unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of a rmlc-like cupin (sfri_3105) from shewanella2 frigidimarina ncimb 400 at 1.90 a resolution

Phyre2

PDB 3jzv chain A

3D model

Region: 26 - 121
Aligned: 88
Modelled: 87
Confidence: 98.0%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein rru_a2000;
PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain.

Phyre2

PDB 1yhf chain A domain 1

3D model

Region: 34 - 124
Aligned: 85
Modelled: 91
Confidence: 98.0%
Identity: 18%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: TM1287-like

Phyre2

PDB 2ozj chain B

3D model

Region: 35 - 121
Aligned: 81
Modelled: 85
Confidence: 97.9%
Identity: 12%
PDB header:unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel;
PDBTitle: crystal structure of a cupin superfamily protein (dsy2733) from2 desulfitobacterium hafniense dcb-2 at 1.60 a resolution

Phyre2

PDB 3kgz chain A

3D model

Region: 63 - 121
Aligned: 59
Modelled: 59
Confidence: 97.8%
Identity: 12%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris

Phyre2
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c3gbgA_
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c1d5yD_
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c2k9sA_
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c3mn2B_
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c3oioA_
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c3oouA_
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c3mklB_
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c1bl0A_
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c3lsgD_
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d1bl0a2
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d1d5ya2
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c1zgwA_
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d1d5ya1
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d1bl0a1
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d2arca_
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c2pfwB_
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c3jzvA_
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d1yhfa1
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c2ozjB_
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c3kgzA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3gbgA_
100.0 15 PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395
2c1d5yD_
99.9 30 PDB header:transcription/dna
Chain: D: PDB Molecule:rob transcription factor;
PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna
3c2k9sA_
99.9 23 PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac
4c3mn2B_
99.9 22 PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
5c3oioA_
99.9 31 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum
6c3oouA_
99.9 21 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua
7c3mklB_
99.9 21 PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
8c1bl0A_
99.9 28 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
9c3lsgD_
99.8 18 PDB header:transcription regulator
Chain: D: PDB Molecule:two-component response regulator yesn;
PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586
10d1bl0a2
99.4 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
11d1d5ya2
99.4 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
12c1zgwA_
98.8 20 PDB header:transcription regulator/dna
Chain: A: PDB Molecule:ada polyprotein;
PDBTitle: nmr structure of e. coli ada protein in complex with dna
13d1d5ya1
98.7 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
14d1bl0a1
98.7 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
15d2arca_
98.7 10 Fold:Double-stranded beta-helix
Superfamily:Regulatory protein AraC
Family:Regulatory protein AraC
16c2pfwB_
98.0 11 PDB header:unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of a rmlc-like cupin (sfri_3105) from shewanella2 frigidimarina ncimb 400 at 1.90 a resolution
17c3jzvA_
98.0 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein rru_a2000;
PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain.
18d1yhfa1
98.0 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
19c2ozjB_
97.9 12 PDB header:unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel;
PDBTitle: crystal structure of a cupin superfamily protein (dsy2733) from2 desulfitobacterium hafniense dcb-2 at 1.60 a resolution
20c3kgzA_
97.8 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris
21d1y9qa2
not modelled 97.8 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Probable transcriptional regulator VC1968, C-terminal domain
22c3ibmB_
not modelled 97.8 12 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of cupin 2 domain-containing protein hhal_0468 from2 halorhodospira halophila
23c3h7yA_
not modelled 97.8 13 PDB header:biosynthetic protein
Chain: A: PDB Molecule:bacilysin biosynthesis protein bacb;
PDBTitle: crystal structure of bacb, an enzyme involved in bacilysin synthesis,2 in tetragonal form
24d1vj2a_
not modelled 97.8 14 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1459-like
25c3fjsC_
not modelled 97.8 15 PDB header:biosynthetic protein
Chain: C: PDB Molecule:uncharacterized protein with rmlc-like cupin fold;
PDBTitle: crystal structure of a putative biosynthetic protein with rmlc-like2 cupin fold (reut_b4087) from ralstonia eutropha jmp134 at 1.90 a3 resolution
26c3cewA_
not modelled 97.7 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized cupin protein;
PDBTitle: crystal structure of a cupin protein (bf4112) from bacteroides2 fragilis. northeast structural genomics consortium target bfr205
27c3rnsA_
not modelled 97.7 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: cupin 2 conserved barrel domain protein from leptotrichia buccalis
28c2gu9B_
not modelled 97.6 6 PDB header:immune system
Chain: B: PDB Molecule:tetracenomycin polyketide synthesis protein;
PDBTitle: crystal structure of xc5357 from xanthomonas campestris: a2 putative tetracenomycin polyketide synthesis protein3 adopting a novel cupin subfamily structure
29c3d82A_
not modelled 97.5 9 PDB header:metal binding protein
Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of a cupin-2 domain containing protein (sfri_3543)2 from shewanella frigidimarina ncimb 400 at 2.05 a resolution
30c3bcwB_
not modelled 97.5 11 PDB header:unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a duf861 family protein with a rmlc-like cupin2 fold (bb1179) from bordetella bronchiseptica rb50 at 1.60 a3 resolution
31d1v70a_
not modelled 97.5 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
32d1y3ta1
not modelled 97.4 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Quercetin 2,3-dioxygenase-like
33d1sq4a_
not modelled 97.4 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
34d1o4ta_
not modelled 97.3 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
35c2vpvA_
not modelled 97.3 7 PDB header:cell cycle
Chain: A: PDB Molecule:protein mif2;
PDBTitle: dimerization domain of mif2p
36c2i45C_
not modelled 97.3 12 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis
37c3i7dB_
not modelled 97.3 12 PDB header:isomerase
Chain: B: PDB Molecule:sugar phosphate isomerase;
PDBTitle: crystal structure of sugar phosphate isomerase from a cupin2 superfamily spo2919 from silicibacter pomeroyi (yp_168127.1) from3 silicibacter pomeroyi dss-3 at 2.30 a resolution
38c2q30C_
not modelled 97.3 13 PDB header:unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a rmlc-like cupin protein (dde_2303) from2 desulfovibrio desulfuricans subsp. at 1.94 a resolution
39d2f4pa1
not modelled 97.3 5 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
40d1rc6a_
not modelled 97.3 7 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
41c3lwcA_
not modelled 97.3 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of structural genomics, unknown function2 (yp_766765.1) from rhizobium leguminosarum bv. viciae 3841 at 1.40 a3 resolution
42c2d40C_
not modelled 97.3 12 PDB header:oxidoreductase
Chain: C: PDB Molecule:putative gentisate 1,2-dioxygenase;
PDBTitle: crystal structure of z3393 from escherichia coli o157:h7
43d1sfna_
not modelled 97.3 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
44d2phda1
not modelled 97.3 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
45d1sefa_
not modelled 97.2 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
46c1sefA_
not modelled 97.2 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of cupin domain protein ef2996 from enterococcus2 faecalis
47c3l2hD_
not modelled 97.2 13 PDB header:isomerase
Chain: D: PDB Molecule:putative sugar phosphate isomerase;
PDBTitle: crystal structure of putative sugar phosphate isomerase (afe_0303)2 from acidithiobacillus ferrooxidans atcc 23270 at 1.85 a resolution
48d2d40a1
not modelled 97.1 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
49d1yfua1
not modelled 97.1 24 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:3-hydroxyanthranilic acid dioxygenase-like
50c2oa2A_
not modelled 97.1 7 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:bh2720 protein;
PDBTitle: crystal structure of bh2720 (10175341) from bacillus halodurans at2 1.41 a resolution
51d1uika1
not modelled 97.1 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
52d1lr5a_
not modelled 97.0 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
53c2o8qA_
not modelled 97.0 15 PDB header:metal binding protein
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of a protein with a cupin-like fold and unknown2 function (bxe_c0505) from burkholderia xenovorans lb400 at 1.55 a3 resolution
54d2pyta1
not modelled 97.0 10 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:EutQ-like
55c2opkC_
not modelled 96.9 19 PDB header:isomerase
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution
56c3h8uA_
not modelled 96.9 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized conserved protein with double-stranded
PDBTitle: crystal structure of uncharacterized conserved protein with double-2 stranded beta-helix domain (yp_001338853.1) from klebsiella3 pneumoniae subsp. pneumoniae mgh 78578 at 1.80 a resolution
57d1zvfa1
not modelled 96.9 22 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:3-hydroxyanthranilic acid dioxygenase-like
58d2b8ma1
not modelled 96.9 5 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:MJ0764-like
59d3bu7a1
not modelled 96.8 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
60c3bu7A_
not modelled 96.8 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:gentisate 1,2-dioxygenase;
PDBTitle: crystal structure and biochemical characterization of gdosp,2 a gentisate 1,2-dioxygenase from silicibacter pomeroyi
61d2bnma2
not modelled 96.7 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1459-like
62d1zrra1
not modelled 96.7 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
63c1y9qA_
not modelled 96.7 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, hth_3 family;
PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
64d1dgwa_
not modelled 96.7 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
65d1j3pa_
not modelled 96.7 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Glucose-6-phosphate isomerase, GPI
66c3ht2A_
not modelled 96.7 14 PDB header:lyase
Chain: A: PDB Molecule:remf protein;
PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus
67d1x82a_
not modelled 96.7 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Glucose-6-phosphate isomerase, GPI
68d1uija1
not modelled 96.7 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
69c3es4B_
not modelled 96.6 19 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein duf861 with a rmlc-like cupin fold;
PDBTitle: crystal structure of protein of unknown function (duf861) with a rmlc-2 like cupin fold (17741406) from agrobacterium tumefaciens str. c583 (dupont) at 1.64 a resolution
70c3myxA_
not modelled 96.6 9 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pspto_0244;
PDBTitle: crystal structure of a pspto_0244 (protein with unknown function which2 belongs to pfam duf861 family) from pseudomonas syringae pv. tomato3 str. dc3000 at 1.30 a resolution
71c2fqpD_
not modelled 96.5 8 PDB header:metal binding protein
Chain: D: PDB Molecule:hypothetical protein bp2299;
PDBTitle: crystal structure of a cupin domain (bp2299) from bordetella pertussis2 tohama i at 1.80 a resolution
72d1o5ua_
not modelled 96.4 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Hypothetical protein TM1112
73d1juha_
not modelled 96.3 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Quercetin 2,3-dioxygenase-like
74d1fxza1
not modelled 96.2 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
75c2bnoA_
not modelled 96.1 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
76d1j58a_
not modelled 96.1 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
77c2oziA_
not modelled 96.0 8 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein rpa4178;
PDBTitle: structural genomics, the crystal structure of a putative2 protein rpa4178 from rhodopseudomonas palustris cga009
78d2phla2
not modelled 96.0 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
79c2vqaC_
not modelled 95.5 7 PDB header:metal-binding protein
Chain: C: PDB Molecule:sll1358 protein;
PDBTitle: protein-folding location can regulate mn versus cu- or zn-2 binding. crystal structure of mnca.
80c3kscD_
not modelled 95.5 19 PDB header:plant protein
Chain: D: PDB Molecule:lega class;
PDBTitle: crystal structure of pea prolegumin, an 11s seed globulin2 from pisum sativum l.
81c2cauA_
not modelled 95.4 17 PDB header:plant protein
Chain: A: PDB Molecule:protein (canavalin);
PDBTitle: canavalin from jack bean
82d1uika2
not modelled 95.4 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
83d2et1a1
not modelled 95.3 7 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
84c1cauB_
not modelled 95.3 19 PDB header:seed storage protein
Chain: B: PDB Molecule:canavalin;
PDBTitle: determination of three crystal structures of canavalin by molecular2 replacement
85c3kglB_
not modelled 95.1 14 PDB header:plant protein
Chain: B: PDB Molecule:cruciferin;
PDBTitle: crystal structure of procruciferin, 11s globulin from2 brassica napus
86c1fxzC_
not modelled 95.0 18 PDB header:plant protein
Chain: C: PDB Molecule:glycinin g1;
PDBTitle: crystal structure of soybean proglycinin a1ab1b homotrimer
87c2eaaB_
not modelled 94.9 11 PDB header:plant protein
Chain: B: PDB Molecule:7s globulin-3;
PDBTitle: crystal structure of adzuki bean 7s globulin-3
88c3es1A_
not modelled 94.9 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of protein with a cupin-like fold and unknown2 function (yp_001165807.1) from novosphingobium aromaticivorans dsm3 12444 at 1.91 a resolution
89c3iwfA_
not modelled 94.7 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator rpir family;
PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
90d1od5a1
not modelled 94.7 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
91c2o3fC_
not modelled 94.7 17 PDB header:transcription
Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh;
PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168.
92d2o3fa1
not modelled 94.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:RpiR-like
93c1uijA_
not modelled 93.9 13 PDB header:sugar binding protein
Chain: A: PDB Molecule:beta subunit of beta conglycinin;
PDBTitle: crystal structure of soybean beta-conglycinin beta2 homotrimer (i122m/k124w)
94d1vr3a1
not modelled 93.8 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
95d2phla1
not modelled 93.8 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
96c2d5fB_
not modelled 93.8 15 PDB header:plant protein
Chain: B: PDB Molecule:glycinin a3b4 subunit;
PDBTitle: crystal structure of recombinant soybean proglycinin a3b4 subunit, its2 comparison with mature glycinin a3b4 subunit, responsible for hexamer3 assembly
97d1uija2
not modelled 93.5 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
98c2e9qA_
not modelled 93.5 18 PDB header:plant protein
Chain: A: PDB Molecule:11s globulin subunit beta;
PDBTitle: recombinant pro-11s globulin of pumpkin
99c3c3vA_
not modelled 93.2 18 PDB header:allergen
Chain: A: PDB Molecule:arachin arah3 isoform;
PDBTitle: crystal structure of peanut major allergen ara h 3
100d1qpza1
not modelled 93.0 9 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
101d1efaa1
not modelled 93.0 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
102d1t56a1
not modelled 92.8 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
103c1vi0B_
not modelled 92.7 21 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator
104c3s7eB_
not modelled 92.7 7 PDB header:allergen
Chain: B: PDB Molecule:allergen ara h 1, clone p41b;
PDBTitle: crystal structure of ara h 1
105d1j5ya1
not modelled 92.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
106c2gfnA_
not modelled 92.3 17 PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional regulator pksa related protein;
PDBTitle: crystal structure of hth-type transcriptional regulator pksa related2 protein from rhodococcus sp. rha1
107d2gfna1
not modelled 92.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
108d2i10a1
not modelled 92.2 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
109d2fbqa1
not modelled 92.1 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
110d1jt6a1
not modelled 92.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
111c3ehkC_
not modelled 91.9 18 PDB header:plant protein
Chain: C: PDB Molecule:prunin;
PDBTitle: crystal structure of pru du amandin, an allergenic protein2 from prunus dulcis
112c3f0cA_
not modelled 91.7 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of transcriptional regulator from cytophaga2 hutchinsonii atcc 33406
113d2hsga1
not modelled 91.6 10 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
114c3iuvA_
not modelled 91.6 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized tetr family protein;
PDBTitle: the structure of a member of tetr family (sco1917) from2 streptomyces coelicolor a3
115c2i10A_
not modelled 91.6 20 PDB header:transcription
Chain: A: PDB Molecule:putative tetr transcriptional regulator;
PDBTitle: putative tetr transcriptional regulator from rhodococcus sp. rha1
116c1jumB_
not modelled 91.6 18 PDB header:transcription
Chain: B: PDB Molecule:hypothetical transcriptional regulator in qaca
PDBTitle: crystal structure of the multidrug binding transcriptional2 repressor qacr bound to the natural drug berberine
117c3e7lD_
not modelled 91.5 25 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
118d2o7ta1
not modelled 91.5 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
119d2fq4a1
not modelled 91.5 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
120d1vi0a1
not modelled 91.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain

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