Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionA4UR84
DateThu Jan 5 10:55:11 GMT 2012
Unique Job ID01bb489e9887b980

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: 90%
252 residues ( 90% 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  MMQPVINAPEIATAREQQLFNGKNFHVFIYNKTESISGLHQHDYYEFTLVLTGRYFQEIN
Secondary structure 
SS confidence 
Disorder  ???????
?
?
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GKRVLLERGDFVFIPLGSHHQSFYEFGATRILNVGISKRFFEQHYLPLLPYCFVASQVYR
Secondary structure 
SS confidence 
Disorder 
????????
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  TNNAFLTYVETVISSLNFRETGLEEFVEMVTFYVINRLRHYREEQVIDDVPQWLKSTVEK
Secondary structure 
SS confidence 
Disorder  ?
?????
??????????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  MHDKEQFSESALENMVALSAKSQEYLTRATQRYYGKTPMQIINEIRINFAKKQLEMTSYS
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280
Sequence  VTDIAFEAGYSSPSLFIKTFKKLTSFTPKSYRKKLTEFNQ
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: 23 - 276
Aligned: 252
Modelled: 254
Confidence: 100.0%
Identity: 13%
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: 171 - 274
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 22%
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 3oou chain A

3D model

Region: 174 - 276
Aligned: 103
Modelled: 103
Confidence: 99.9%
Identity: 27%
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 3oio chain A

3D model

Region: 168 - 277
Aligned: 110
Modelled: 110
Confidence: 99.9%
Identity: 22%
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 1bl0 chain A

3D model

Region: 171 - 277
Aligned: 107
Modelled: 107
Confidence: 99.9%
Identity: 19%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex

Phyre2

PDB 3mkl chain B

3D model

Region: 167 - 277
Aligned: 110
Modelled: 111
Confidence: 99.9%
Identity: 19%
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 3mn2 chain B

3D model

Region: 174 - 276
Aligned: 103
Modelled: 103
Confidence: 99.9%
Identity: 21%
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 2k9s chain A

3D model

Region: 172 - 274
Aligned: 103
Modelled: 103
Confidence: 99.9%
Identity: 17%
PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac

Phyre2

PDB 3lsg chain D

3D model

Region: 176 - 264
Aligned: 89
Modelled: 89
Confidence: 99.8%
Identity: 20%
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 1d5y chain A domain 2

3D model

Region: 226 - 274
Aligned: 49
Modelled: 49
Confidence: 99.5%
Identity: 31%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1bl0 chain A domain 2

3D model

Region: 226 - 273
Aligned: 48
Modelled: 48
Confidence: 99.5%
Identity: 21%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 2arc chain A

3D model

Region: 39 - 162
Aligned: 124
Modelled: 124
Confidence: 98.9%
Identity: 14%
Fold: Double-stranded beta-helix
Superfamily: Regulatory protein AraC
Family: Regulatory protein AraC

Phyre2

PDB 1bl0 chain A domain 1

3D model

Region: 171 - 223
Aligned: 53
Modelled: 53
Confidence: 98.8%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1d5y chain A domain 1

3D model

Region: 171 - 223
Aligned: 53
Modelled: 53
Confidence: 98.8%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1zgw chain A

3D model

Region: 158 - 229
Aligned: 70
Modelled: 72
Confidence: 98.7%
Identity: 17%
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 3ibm chain B

3D model

Region: 32 - 99
Aligned: 68
Modelled: 68
Confidence: 98.7%
Identity: 16%
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

Phyre2

PDB 3kgz chain A

3D model

Region: 37 - 99
Aligned: 63
Modelled: 63
Confidence: 98.6%
Identity: 21%
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

PDB 3jzv chain A

3D model

Region: 37 - 99
Aligned: 63
Modelled: 63
Confidence: 98.5%
Identity: 21%
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 1yfu chain A domain 1

3D model

Region: 19 - 94
Aligned: 76
Modelled: 76
Confidence: 98.5%
Identity: 20%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: 3-hydroxyanthranilic acid dioxygenase-like

Phyre2

PDB 3h7y chain A

3D model

Region: 24 - 102
Aligned: 79
Modelled: 79
Confidence: 98.5%
Identity: 11%
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

Phyre2

PDB 2ozj chain B

3D model

Region: 5 - 97
Aligned: 93
Modelled: 91
Confidence: 98.4%
Identity: 14%
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
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c3gbgA_
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c1d5yD_
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c3oouA_
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c3oioA_
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c1bl0A_
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c3mklB_
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c3mn2B_
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c2k9sA_
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c3lsgD_
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d1d5ya2
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d1bl0a2
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d2arca_
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d1bl0a1
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d1d5ya1
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c1zgwA_
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c3ibmB_
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c3kgzA_
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c3jzvA_
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d1yfua1
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c3h7yA_
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c2ozjB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3gbgA_
100.0 13 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 22 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
3c3oouA_
99.9 27 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua
4c3oioA_
99.9 22 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
5c1bl0A_
99.9 19 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
6c3mklB_
99.9 19 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
7c3mn2B_
99.9 21 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
8c2k9sA_
99.9 17 PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac
9c3lsgD_
99.8 20 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
10d1d5ya2
99.5 31 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
11d1bl0a2
99.5 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
12d2arca_
98.9 14 Fold:Double-stranded beta-helix
Superfamily:Regulatory protein AraC
Family:Regulatory protein AraC
13d1bl0a1
98.8 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
14d1d5ya1
98.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
15c1zgwA_
98.7 17 PDB header:transcription regulator/dna
Chain: A: PDB Molecule:ada polyprotein;
PDBTitle: nmr structure of e. coli ada protein in complex with dna
16c3ibmB_
98.7 16 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
17c3kgzA_
98.6 21 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
18c3jzvA_
98.5 21 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.
19d1yfua1
98.5 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:3-hydroxyanthranilic acid dioxygenase-like
20c3h7yA_
98.5 11 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
21d1vj2a_
not modelled 98.5 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1459-like
22c2ozjB_
98.4 14 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
23d1y9qa2
not modelled 98.3 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Probable transcriptional regulator VC1968, C-terminal domain
24c3cewA_
not modelled 98.3 19 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
25c3fjsC_
not modelled 98.3 16 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
26d1y3ta1
not modelled 98.3 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Quercetin 2,3-dioxygenase-like
27c2gu9B_
not modelled 98.2 14 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
28d1lr5a_
not modelled 98.2 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
29c2pfwB_
not modelled 98.2 21 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
30d1o4ta_
not modelled 98.2 28 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
31c1sefA_
not modelled 98.2 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of cupin domain protein ef2996 from enterococcus2 faecalis
32d1sefa_
not modelled 98.2 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
33c3bu7A_
not modelled 98.2 15 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
34d3bu7a1
not modelled 98.2 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
35c3d82A_
not modelled 98.2 21 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
36d1sfna_
not modelled 98.2 10 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
37d1sq4a_
not modelled 98.2 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
38d1uika1
not modelled 98.2 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
39c3l2hD_
not modelled 98.1 23 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
40c3rnsA_
not modelled 98.1 20 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
41c2o8qA_
not modelled 98.1 23 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
42c2d40C_
not modelled 98.1 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:putative gentisate 1,2-dioxygenase;
PDBTitle: crystal structure of z3393 from escherichia coli o157:h7
43d2b8ma1
not modelled 98.1 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:MJ0764-like
44c3i7dB_
not modelled 98.1 21 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
45d1yhfa1
not modelled 98.1 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
46d1v70a_
not modelled 98.1 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
47d1uija1
not modelled 98.1 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
48d1zvfa1
not modelled 98.1 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:3-hydroxyanthranilic acid dioxygenase-like
49d2phda1
not modelled 98.1 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
50d2d40a1
not modelled 98.0 10 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
51d2f4pa1
not modelled 98.0 22 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
52c2oa2A_
not modelled 98.0 19 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
53c2i45C_
not modelled 98.0 21 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis
54c3ht2A_
not modelled 98.0 25 PDB header:lyase
Chain: A: PDB Molecule:remf protein;
PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus
55c3bcwB_
not modelled 98.0 15 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
56d1rc6a_
not modelled 97.9 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
57c2vpvA_
not modelled 97.9 13 PDB header:cell cycle
Chain: A: PDB Molecule:protein mif2;
PDBTitle: dimerization domain of mif2p
58c3h8uA_
not modelled 97.9 18 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
59d1zrra1
not modelled 97.9 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
60d1dgwa_
not modelled 97.8 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
61d1juha_
not modelled 97.8 23 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Quercetin 2,3-dioxygenase-like
62d1x82a_
not modelled 97.7 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Glucose-6-phosphate isomerase, GPI
63c3lwcA_
not modelled 97.7 16 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
64c1y9qA_
not modelled 97.7 16 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
65d1fxza1
not modelled 97.7 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
66c2q30C_
not modelled 97.6 15 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
67d1j3pa_
not modelled 97.6 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Glucose-6-phosphate isomerase, GPI
68c3es1A_
not modelled 97.6 15 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
69c2fqpD_
not modelled 97.6 18 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
70c1uijA_
not modelled 97.5 19 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)
71d2bnma2
not modelled 97.5 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1459-like
72d1j58a_
not modelled 97.4 25 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
73d2phla1
not modelled 97.4 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
74c2vqaC_
not modelled 97.4 21 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.
75d1o5ua_
not modelled 97.4 25 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Hypothetical protein TM1112
76c2eaaB_
not modelled 97.4 17 PDB header:plant protein
Chain: B: PDB Molecule:7s globulin-3;
PDBTitle: crystal structure of adzuki bean 7s globulin-3
77c2oziA_
not modelled 97.4 18 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
78c2opkC_
not modelled 97.3 14 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
79c3s7eB_
not modelled 97.3 14 PDB header:allergen
Chain: B: PDB Molecule:allergen ara h 1, clone p41b;
PDBTitle: crystal structure of ara h 1
80d2pyta1
not modelled 97.2 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:EutQ-like
81d2et1a1
not modelled 97.2 23 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
82c1cauB_
not modelled 97.2 19 PDB header:seed storage protein
Chain: B: PDB Molecule:canavalin;
PDBTitle: determination of three crystal structures of canavalin by molecular2 replacement
83c1fxzC_
not modelled 97.1 13 PDB header:plant protein
Chain: C: PDB Molecule:glycinin g1;
PDBTitle: crystal structure of soybean proglycinin a1ab1b homotrimer
84d2phla2
not modelled 97.1 14 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
85c2bnoA_
not modelled 96.9 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
86d1fxza2
not modelled 96.9 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
87d1vr3a1
not modelled 96.8 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
88d1od5a1
not modelled 96.7 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
89d1uika2
not modelled 96.7 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
90c2cauA_
not modelled 96.7 20 PDB header:plant protein
Chain: A: PDB Molecule:protein (canavalin);
PDBTitle: canavalin from jack bean
91c3kglB_
not modelled 96.7 8 PDB header:plant protein
Chain: B: PDB Molecule:cruciferin;
PDBTitle: crystal structure of procruciferin, 11s globulin from2 brassica napus
92d1od5a2
not modelled 96.6 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
93c3myxA_
not modelled 96.6 16 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
94c3ebrA_
not modelled 96.4 8 PDB header:unknown function
Chain: A: PDB Molecule:uncharacterized rmlc-like cupin;
PDBTitle: crystal structure of an rmlc-like cupin protein (reut_a0381) from2 ralstonia eutropha jmp134 at 2.60 a resolution
95c3kscD_
not modelled 96.4 12 PDB header:plant protein
Chain: D: PDB Molecule:lega class;
PDBTitle: crystal structure of pea prolegumin, an 11s seed globulin2 from pisum sativum l.
96d1uija2
not modelled 96.3 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
97c2d5fB_
not modelled 96.2 17 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
98c3o14B_
not modelled 96.2 23 PDB header:gene regulation
Chain: B: PDB Molecule:anti-ecfsigma factor, chrr;
PDBTitle: crystal structure of an anti-ecfsigma factor, chrr (maqu_0586) from2 marinobacter aquaeolei vt8 at 1.70 a resolution
99c3es4B_
not modelled 96.1 16 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
100c2e9qA_
not modelled 96.0 20 PDB header:plant protein
Chain: A: PDB Molecule:11s globulin subunit beta;
PDBTitle: recombinant pro-11s globulin of pumpkin
101c3c3vA_
not modelled 95.9 16 PDB header:allergen
Chain: A: PDB Molecule:arachin arah3 isoform;
PDBTitle: crystal structure of peanut major allergen ara h 3
102d2hsga1
not modelled 95.5 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
103c3ehkC_
not modelled 95.2 13 PDB header:plant protein
Chain: C: PDB Molecule:prunin;
PDBTitle: crystal structure of pru du amandin, an allergenic protein2 from prunus dulcis
104c2qnkA_
not modelled 95.2 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:3-hydroxyanthranilate 3,4-dioxygenase;
PDBTitle: crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase
105c3balB_
not modelled 95.1 10 PDB header:oxidoreductase
Chain: B: PDB Molecule:acetylacetone-cleaving enzyme;
PDBTitle: crystal structure of an acetylacetone dioxygenase from2 acinetobacter johnsonii
106d2bjca1
not modelled 95.0 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
107d1sgma1
not modelled 95.0 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
108d1efaa1
not modelled 94.9 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
109c2xlfA_
not modelled 94.9 16 PDB header:metal binding protein
Chain: A: PDB Molecule:sll1785 protein;
PDBTitle: structure and metal-loading of a soluble periplasm cupro-protein:2 apo-cuca-closed (semet)
110c3h5tA_
not modelled 94.7 21 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
111d1qpza1
not modelled 94.7 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
112c3cjxE_
not modelled 94.6 14 PDB header:unknown function
Chain: E: PDB Molecule:protein of unknown function with a cupin-like fold;
PDBTitle: crystal structure of a protein of unknown function with a cupin-like2 fold (reut_b4571) from ralstonia eutropha jmp134 at 2.60 a resolution
113d1eyba_
not modelled 94.6 10 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Homogentisate dioxygenase
114c1ey2A_
not modelled 94.6 10 PDB header:oxidoreductase
Chain: A: PDB Molecule:homogentisate 1,2-dioxygenase;
PDBTitle: human homogentisate dioxygenase with fe(ii)
115d1ui5a1
not modelled 94.4 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
116c3on4D_
not modelled 94.4 7 PDB header:transcription
Chain: D: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of tetr transcriptional regulator from legionella2 pneumophila
117d1jt6a1
not modelled 94.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
118c1vi0B_
not modelled 94.3 2 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator
119c1sgmA_
not modelled 94.2 13 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator yxaf;
PDBTitle: crystal structure of hypothetical protein yxaf
120d2np5a1
not modelled 94.2 6 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