Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP07003
DateThu Jan 5 10:59:55 GMT 2012
Unique Job ID277737d5848502c9

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3eyaE_
Top template information
PDB header:oxidoreductase
Chain: E: PDB Molecule:pyruvate dehydrogenase [cytochrome];
PDBTitle: structural basis for membrane binding and catalytic2 activation of the peripheral membrane enzyme pyruvate3 oxidase from escherichia coli
Confidence and coverage
Confidence:100.0% Coverage: 91%
522 residues ( 91% 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  MKQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEEVAAFAAGAE
Secondary structure 
SS confidence 
Disorder  ????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  AQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAHIPSSEIGSGYFQETHPQEL
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  FRECSHYCELVSSPEQIPQVLAIAMRKAVLNRGVSVVVLPGDVALKPAPEGATMHWYHAP
Secondary structure 
SS confidence 
Disorder 
????????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  QPVVTPEEEELRKLAQLLRYSSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHV
Secondary structure 
SS confidence 
Disorder  ???
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  EYDNPYDVGMTGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  HSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAKPSEKAIHPQ
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  YLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLGSFNHGSMANAMPQALGAQA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  TEPERQVVAMCGDGGFSMLMGDFLSVVQMKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGT
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  ELHDTNFARIAEACGITGIRVEKASEVDEALQRAFSIDGPVLVDVVVAKEELAIPPQIKL
Secondary structure 
SS confidence 
Disorder 
?
???????
Disorder confidence 
 
   .........550.........560.........570..
Sequence  EQAKGFSLYMLRAIISGRGDEVIELAKTNWLR
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 3eya chain E

3D model

Region: 1 - 536
Aligned: 522
Modelled: 522
Confidence: 100.0%
Identity: 100%
PDB header:oxidoreductase
Chain: E: PDB Molecule:pyruvate dehydrogenase [cytochrome];
PDBTitle: structural basis for membrane binding and catalytic2 activation of the peripheral membrane enzyme pyruvate3 oxidase from escherichia coli

Phyre2

PDB 1pow chain A

3D model

Region: 2 - 568
Aligned: 566
Modelled: 567
Confidence: 100.0%
Identity: 29%
PDB header:oxidoreductase(oxygen as acceptor)
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: the refined structures of a stabilized mutant and of wild-type2 pyruvate oxidase from lactobacillus plantarum

Phyre2

PDB 2dji chain A

3D model

Region: 2 - 555
Aligned: 553
Modelled: 554
Confidence: 100.0%
Identity: 29%
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: crystal structure of pyruvate oxidase from aerococcus2 viridans containing fad

Phyre2

PDB 1yi1 chain A

3D model

Region: 1 - 536
Aligned: 535
Modelled: 536
Confidence: 100.0%
Identity: 28%
PDB header:transferase
Chain: A: PDB Molecule:acetolactate synthase;
PDBTitle: crystal structure of arabidopsis thaliana acetohydroxyacid synthase in2 complex with a sulfonylurea herbicide, tribenuron methyl

Phyre2

PDB 2pgn chain A

3D model

Region: 3 - 538
Aligned: 536
Modelled: 536
Confidence: 100.0%
Identity: 21%
PDB header:hydrolase
Chain: A: PDB Molecule:cyclohexane-1,2-dione hydrolase (cdh);
PDBTitle: the crystal structure of fad and thdp-dependent cyclohexane-1,2-dione2 hydrolase in complex with cyclohexane-1,2-dione

Phyre2

PDB 1t9d chain B

3D model

Region: 1 - 536
Aligned: 523
Modelled: 524
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: B: PDB Molecule:acetolactate synthase, mitochondrial;
PDBTitle: crystal structure of yeast acetohydroxyacid synthase in2 complex with a sulfonylurea herbicide, metsulfuron methyl

Phyre2

PDB 2pan chain F

3D model

Region: 2 - 546
Aligned: 543
Modelled: 540
Confidence: 100.0%
Identity: 24%
PDB header:lyase
Chain: F: PDB Molecule:glyoxylate carboligase;
PDBTitle: crystal structure of e. coli glyoxylate carboligase

Phyre2

PDB 1ozh chain D

3D model

Region: 3 - 535
Aligned: 521
Modelled: 533
Confidence: 100.0%
Identity: 25%
PDB header:lyase
Chain: D: PDB Molecule:acetolactate synthase, catabolic;
PDBTitle: the crystal structure of klebsiella pneumoniae acetolactate2 synthase with enzyme-bound cofactor and with an unusual3 intermediate.

Phyre2

PDB 1jsc chain A

3D model

Region: 1 - 530
Aligned: 513
Modelled: 515
Confidence: 100.0%
Identity: 25%
PDB header:lyase
Chain: A: PDB Molecule:acetohydroxy-acid synthase;
PDBTitle: crystal structure of the catalytic subunit of yeast2 acetohydroxyacid synthase: a target for herbicidal3 inhibitors

Phyre2

PDB 2ag1 chain A

3D model

Region: 2 - 537
Aligned: 532
Modelled: 535
Confidence: 100.0%
Identity: 22%
PDB header:lyase
Chain: A: PDB Molecule:benzaldehyde lyase;
PDBTitle: crystal structure of benzaldehyde lyase (bal)- semet

Phyre2

PDB 2ji6 chain B

3D model

Region: 1 - 539
Aligned: 529
Modelled: 539
Confidence: 100.0%
Identity: 21%
PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: x-ray structure of oxalyl-coa decarboxylase in complex with2 3-deaza-thdp and oxalyl-coa

Phyre2

PDB 1zpd chain A

3D model

Region: 2 - 535
Aligned: 519
Modelled: 534
Confidence: 100.0%
Identity: 21%
PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis

Phyre2

PDB 2q27 chain B

3D model

Region: 1 - 533
Aligned: 524
Modelled: 533
Confidence: 100.0%
Identity: 22%
PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: crystal structure of oxalyl-coa decarboxylase from escherichia coli

Phyre2

PDB 2v3w chain C

3D model

Region: 4 - 528
Aligned: 510
Modelled: 525
Confidence: 100.0%
Identity: 21%
PDB header:lyase
Chain: C: PDB Molecule:benzoylformate decarboxylase;
PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida

Phyre2

PDB 2x7j chain A

3D model

Region: 4 - 554
Aligned: 546
Modelled: 551
Confidence: 100.0%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene
PDBTitle: structure of the menaquinone biosynthesis protein mend from2 bacillus subtilis

Phyre2

PDB 2vbi chain F

3D model

Region: 2 - 533
Aligned: 513
Modelled: 532
Confidence: 100.0%
Identity: 19%
PDB header:lyase
Chain: F: PDB Molecule:pyruvate decarboxylase;
PDBTitle: holostructure of pyruvate decarboxylase from acetobacter2 pasteurianus

Phyre2

PDB 2vbg chain B

3D model

Region: 1 - 553
Aligned: 516
Modelled: 537
Confidence: 100.0%
Identity: 22%
PDB header:lyase
Chain: B: PDB Molecule:branched-chain alpha-ketoacid decarboxylase;
PDBTitle: the complex structure of the branched-chain keto acid2 decarboxylase (kdca) from lactococcus lactis with 2r-1-3 hydroxyethyl-deazathdp

Phyre2

PDB 1upa chain C

3D model

Region: 4 - 530
Aligned: 525
Modelled: 527
Confidence: 100.0%
Identity: 20%
PDB header:synthase
Chain: C: PDB Molecule:carboxyethylarginine synthase;
PDBTitle: carboxyethylarginine synthase from streptomyces2 clavuligerus (semet structure)

Phyre2

PDB 1ovm chain C

3D model

Region: 3 - 549
Aligned: 512
Modelled: 512
Confidence: 100.0%
Identity: 20%
PDB header:lyase
Chain: C: PDB Molecule:indole-3-pyruvate decarboxylase;
PDBTitle: crystal structure of indolepyruvate decarboxylase from2 enterobacter cloacae

Phyre2

PDB 2w93 chain A

3D model

Region: 2 - 533
Aligned: 508
Modelled: 528
Confidence: 100.0%
Identity: 17%
PDB header:lyase
Chain: A: PDB Molecule:pyruvate decarboxylase isozyme 1;
PDBTitle: crystal structure of the saccharomyces cerevisiae pyruvate2 decarboxylase variant e477q in complex with the surrogate3 pyruvamide

Phyre2
1
c3eyaE_
2
c1powA_
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c2djiA_
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c1yi1A_
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c2pgnA_
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c1t9dB_
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c2panF_
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c1ozhD_
9
c1jscA_
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c2ag1A_
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c2ji6B_
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c1zpdA_
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c2q27B_
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c2v3wC_
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c2x7jA_
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c2vbiF_
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c2vbgB_
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c1upaC_
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c1ovmC_
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c2w93A_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3eyaE_
100.0 100 PDB header:oxidoreductase
Chain: E: PDB Molecule:pyruvate dehydrogenase [cytochrome];
PDBTitle: structural basis for membrane binding and catalytic2 activation of the peripheral membrane enzyme pyruvate3 oxidase from escherichia coli
2c1powA_
100.0 29 PDB header:oxidoreductase(oxygen as acceptor)
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: the refined structures of a stabilized mutant and of wild-type2 pyruvate oxidase from lactobacillus plantarum
3c2djiA_
100.0 29 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: crystal structure of pyruvate oxidase from aerococcus2 viridans containing fad
4c1yi1A_
100.0 28 PDB header:transferase
Chain: A: PDB Molecule:acetolactate synthase;
PDBTitle: crystal structure of arabidopsis thaliana acetohydroxyacid synthase in2 complex with a sulfonylurea herbicide, tribenuron methyl
5c2pgnA_
100.0 21 PDB header:hydrolase
Chain: A: PDB Molecule:cyclohexane-1,2-dione hydrolase (cdh);
PDBTitle: the crystal structure of fad and thdp-dependent cyclohexane-1,2-dione2 hydrolase in complex with cyclohexane-1,2-dione
6c1t9dB_
100.0 25 PDB header:transferase
Chain: B: PDB Molecule:acetolactate synthase, mitochondrial;
PDBTitle: crystal structure of yeast acetohydroxyacid synthase in2 complex with a sulfonylurea herbicide, metsulfuron methyl
7c2panF_
100.0 24 PDB header:lyase
Chain: F: PDB Molecule:glyoxylate carboligase;
PDBTitle: crystal structure of e. coli glyoxylate carboligase
8c1ozhD_
100.0 25 PDB header:lyase
Chain: D: PDB Molecule:acetolactate synthase, catabolic;
PDBTitle: the crystal structure of klebsiella pneumoniae acetolactate2 synthase with enzyme-bound cofactor and with an unusual3 intermediate.
9c1jscA_
100.0 25 PDB header:lyase
Chain: A: PDB Molecule:acetohydroxy-acid synthase;
PDBTitle: crystal structure of the catalytic subunit of yeast2 acetohydroxyacid synthase: a target for herbicidal3 inhibitors
10c2ag1A_
100.0 22 PDB header:lyase
Chain: A: PDB Molecule:benzaldehyde lyase;
PDBTitle: crystal structure of benzaldehyde lyase (bal)- semet
11c2ji6B_
100.0 21 PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: x-ray structure of oxalyl-coa decarboxylase in complex with2 3-deaza-thdp and oxalyl-coa
12c1zpdA_
100.0 21 PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis
13c2q27B_
100.0 22 PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: crystal structure of oxalyl-coa decarboxylase from escherichia coli
14c2v3wC_
100.0 21 PDB header:lyase
Chain: C: PDB Molecule:benzoylformate decarboxylase;
PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida
15c2x7jA_
100.0 13 PDB header:transferase
Chain: A: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene
PDBTitle: structure of the menaquinone biosynthesis protein mend from2 bacillus subtilis
16c2vbiF_
100.0 19 PDB header:lyase
Chain: F: PDB Molecule:pyruvate decarboxylase;
PDBTitle: holostructure of pyruvate decarboxylase from acetobacter2 pasteurianus
17c2vbgB_
100.0 22 PDB header:lyase
Chain: B: PDB Molecule:branched-chain alpha-ketoacid decarboxylase;
PDBTitle: the complex structure of the branched-chain keto acid2 decarboxylase (kdca) from lactococcus lactis with 2r-1-3 hydroxyethyl-deazathdp
18c1upaC_
100.0 20 PDB header:synthase
Chain: C: PDB Molecule:carboxyethylarginine synthase;
PDBTitle: carboxyethylarginine synthase from streptomyces2 clavuligerus (semet structure)
19c1ovmC_
100.0 20 PDB header:lyase
Chain: C: PDB Molecule:indole-3-pyruvate decarboxylase;
PDBTitle: crystal structure of indolepyruvate decarboxylase from2 enterobacter cloacae
20c2w93A_
100.0 17 PDB header:lyase
Chain: A: PDB Molecule:pyruvate decarboxylase isozyme 1;
PDBTitle: crystal structure of the saccharomyces cerevisiae pyruvate2 decarboxylase variant e477q in complex with the surrogate3 pyruvamide
21c2nxwB_
not modelled 100.0 19 PDB header:lyase
Chain: B: PDB Molecule:phenyl-3-pyruvate decarboxylase;
PDBTitle: crystal structure of phenylpyruvate decarboxylase of azospirillum2 brasilense
22c2jlaD_
not modelled 100.0 13 PDB header:transferase
Chain: D: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene
PDBTitle: crystal structure of e.coli mend, 2-succinyl-5-enolpyruvyl-2 6-hydroxy-3-cyclohexadiene-1-carboxylate synthase - semet3 protein
23c3lq1A_
not modelled 100.0 17 PDB header:transferase
Chain: A: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-
PDBTitle: crystal structure of 2-succinyl-6-hydroxy-2,4-cyclohexadiene2 1-carboxylic acid synthase/2-oxoglutarate decarboxylase3 from listeria monocytogenes str. 4b f2365
24d2djia3
not modelled 100.0 29 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
25d2ez9a3
not modelled 100.0 29 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
26d1t9ba3
not modelled 100.0 32 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
27d1ybha3
not modelled 100.0 32 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
28d1ozha3
not modelled 100.0 28 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
29d2djia2
not modelled 100.0 32 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
30d1ybha2
not modelled 100.0 30 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
31d1t9ba2
not modelled 100.0 23 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
32d1zpda2
not modelled 100.0 19 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
33d1q6za2
not modelled 100.0 16 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
34d1ozha2
not modelled 100.0 27 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
35d1pvda2
not modelled 100.0 20 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
36d1ovma3
not modelled 100.0 22 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
37d2ihta3
not modelled 100.0 22 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
38d2ihta2
not modelled 100.0 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
39d2ji7a2
not modelled 100.0 21 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
40d2ez9a2
not modelled 100.0 35 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
41d1zpda3
not modelled 100.0 22 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
42d2ji7a3
not modelled 100.0 19 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
43d1q6za3
not modelled 100.0 24 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
44d1ovma2
not modelled 100.0 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
45d1pvda3
not modelled 100.0 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
46d1jsca3
not modelled 100.0 35 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
47d2ez9a1
not modelled 100.0 23 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
48d2djia1
not modelled 100.0 26 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
49d1t9ba1
not modelled 100.0 21 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
50d1ozha1
not modelled 99.9 22 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
51d1ybha1
not modelled 99.9 25 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
52d2ji7a1
not modelled 99.9 21 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
53d2ihta1
not modelled 99.9 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
54d1q6za1
not modelled 99.9 24 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
55d1zpda1
not modelled 99.9 21 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
56d1ovma1
not modelled 99.9 17 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
57d1pvda1
not modelled 99.9 13 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
58c2c3yA_
not modelled 99.9 10 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase;
PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus
59d2c42a1
not modelled 99.8 12 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:PFOR Pyr module
60d2c42a2
not modelled 99.7 20 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:PFOR PP module
61c3cf4G_
not modelled 99.6 15 PDB header:oxidoreductase
Chain: G: PDB Molecule:acetyl-coa decarboxylase/synthase epsilon subunit;
PDBTitle: structure of the codh component of the m. barkeri acds complex
62d2bfda1
not modelled 99.6 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
63d2r8oa2
not modelled 99.6 21 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
64d2ozla1
not modelled 99.6 19 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
65d1w85a_
not modelled 99.6 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
66d1gpua1
not modelled 99.5 20 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
67d1umda_
not modelled 99.5 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
68d1r9ja2
not modelled 99.5 18 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
69d1itza1
not modelled 99.5 18 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
70c1yd7A_
not modelled 99.4 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-keto acid:ferredoxin oxidoreductase subunit
PDBTitle: conserved hypothetical protein pfu-1647980-001 from2 pyrococcus furiosus
71c2o1xA_
not modelled 99.3 23 PDB header:transferase
Chain: A: PDB Molecule:1-deoxy-d-xylulose-5-phosphate synthase;
PDBTitle: 1-deoxy-d-xylulose 5-phosphate synthase (dxs) from2 deinococcus radiodurans
72c3m7iA_
not modelled 99.3 18 PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: crystal structure of transketolase in complex with thiamine2 diphosphate, ribose-5-phosphate(pyranose form) and3 magnesium ion
73c2o1sC_
not modelled 99.3 20 PDB header:transferase
Chain: C: PDB Molecule:1-deoxy-d-xylulose-5-phosphate synthase;
PDBTitle: 1-deoxy-d-xylulose 5-phosphate synthase (dxs) from2 escherichia coli
74c2e6kB_
not modelled 99.3 18 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: x-ray structure of thermus thermopilus hb8 tt0505
75c3hylB_
not modelled 99.3 19 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of transketolase from bacillus anthracis
76c3uk1A_
not modelled 99.2 21 PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: crystal structure of a transketolase from burkholderia thailandensis2 with an oxidized cysteinesulfonic acid in the active site
77c1itzC_
not modelled 99.2 19 PDB header:transferase
Chain: C: PDB Molecule:transketolase;
PDBTitle: maize transketolase in complex with tpp
78c1tkcA_
not modelled 99.2 20 PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: specificity of coenzyme binding in thiamin diphosphate2 dependent enzymes: crystal structures of yeast3 transketolase in complex with analogs of thiamin4 diphosphate
79c1r9jB_
not modelled 99.2 18 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: transketolase from leishmania mexicana
80c3mosA_
not modelled 99.2 22 PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: the structure of human transketolase
81d1qs0a_
not modelled 99.2 22 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
82c2r8pA_
not modelled 99.2 20 PDB header:transferase
Chain: A: PDB Molecule:transketolase 1;
PDBTitle: transketolase from e. coli in complex with substrate d-2 fructose-6-phosphate
83c3komB_
not modelled 99.1 19 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of apo transketolase from francisella tularensis
84c2g28A_
not modelled 99.1 25 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate dehydrogenase e1 component;
PDBTitle: e. coli pyruvate dehydrogenase h407a variant2 phosphonolactylthiamin diphosphate complex
85d2ieaa2
not modelled 99.0 26 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
86c3ahhA_
not modelled 98.8 18 PDB header:lyase
Chain: A: PDB Molecule:xylulose 5-phosphate/fructose 6-phosphate phosphoketolase;
PDBTitle: h142a mutant of phosphoketolase from bifidobacterium breve complexed2 with acetyl thiamine diphosphate
87c1olsB_
not modelled 98.2 14 PDB header:oxidoreductase
Chain: B: PDB Molecule:2-oxoisovalerate dehydrogenase beta subunit;
PDBTitle: roles of his291-alpha and his146-beta' in the reductive2 acylation reaction catalyzed by human branched-chain3 alpha-ketoacid dehydrogenase
88c1ni4D_
not modelled 98.1 12 PDB header:oxidoreductase
Chain: D: PDB Molecule:pyruvate dehydrogenase e1 component: beta
PDBTitle: human pyruvate dehydrogenase
89c2jgdA_
not modelled 98.0 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-oxoglutarate dehydrogenase e1 component;
PDBTitle: e. coli 2-oxoglutarate dehydrogenase (e1o)
90c2bp7F_
not modelled 98.0 12 PDB header:oxidoreductase
Chain: F: PDB Molecule:2-oxoisovalerate dehydrogenase beta subunit;
PDBTitle: new crystal form of the pseudomonas putida branched-chain2 dehydrogenase (e1)
91c3k35D_
not modelled 97.9 23 PDB header:hydrolase
Chain: D: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: crystal structure of human sirt6
92c3pkiF_
not modelled 97.8 24 PDB header:hydrolase
Chain: F: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: human sirt6 crystal structure in complex with adp ribose
93d1gpua2
not modelled 97.8 10 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
94c1efpC_
not modelled 97.7 21 PDB header:electron transport
Chain: C: PDB Molecule:protein (electron transfer flavoprotein);
PDBTitle: electron transfer flavoprotein (etf) from paracoccus2 denitrificans
95d2r8oa1
not modelled 97.6 9 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
96c2yicC_
not modelled 97.6 16 PDB header:lyase
Chain: C: PDB Molecule:2-oxoglutarate decarboxylase;
PDBTitle: crystal structure of the suca domain of mycobacterium smegmatis2 alpha-ketoglutarate decarboxylase (triclinic form)
97d1r9ja1
not modelled 97.6 13 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
98d1itza2
not modelled 97.4 11 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
99d2ozlb1
not modelled 97.3 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
100d1efva2
not modelled 97.3 17 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:C-terminal domain of the electron transfer flavoprotein alpha subunit
101d1ytla1
not modelled 97.2 13 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:ACDE2-like
102c3dufD_
not modelled 97.2 11 PDB header:oxidoreductase/transferase
Chain: D: PDB Molecule:pyruvate dehydrogenase e1 component subunit beta;
PDBTitle: snapshots of catalysis in the e1 subunit of the pyruvate2 dehydrogenase multi-enzyme complex
103d1efpa2
not modelled 97.0 21 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:C-terminal domain of the electron transfer flavoprotein alpha subunit
104d3clsd2
not modelled 97.0 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:C-terminal domain of the electron transfer flavoprotein alpha subunit
105d1w85b1
not modelled 97.0 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
106c1um9D_
not modelled 97.0 16 PDB header:oxidoreductase
Chain: D: PDB Molecule:2-oxo acid dehydrogenase beta subunit;
PDBTitle: branched-chain 2-oxo acid dehydrogenase (e1) from thermus2 thermophilus hb8 in apo-form
107c1ik6A_
not modelled 96.9 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate dehydrogenase;
PDBTitle: 3d structure of the e1beta subunit of pyruvate2 dehydrogenase from the archeon pyrobaculum aerophilum
108d1umdb1
not modelled 96.6 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
109c2xt6B_
not modelled 96.5 17 PDB header:lyase
Chain: B: PDB Molecule:2-oxoglutarate decarboxylase;
PDBTitle: crystal structure of mycobacterium smegmatis alpha-ketoglutarate2 decarboxylase homodimer (orthorhombic form)
110d1qs0b1
not modelled 96.4 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
111c3glsC_
not modelled 96.4 18 PDB header:hydrolase
Chain: C: PDB Molecule:nad-dependent deacetylase sirtuin-3,
PDBTitle: crystal structure of human sirt3
112c2hjhB_
not modelled 96.3 18 PDB header:hydrolase
Chain: B: PDB Molecule:nad-dependent histone deacetylase sir2;
PDBTitle: crystal structure of the sir2 deacetylase
113d1j8fa_
not modelled 96.0 20 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
114c1q14A_
not modelled 96.0 11 PDB header:hydrolase
Chain: A: PDB Molecule:hst2 protein;
PDBTitle: structure and autoregulation of the yeast hst2 homolog of sir2
115d1m2ka_
not modelled 95.9 19 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
116d1yc5a1
not modelled 95.9 11 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
117d1s5pa_
not modelled 95.8 13 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
118d1ma3a_
not modelled 95.7 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
119d2b4ya1
not modelled 95.7 11 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
120c1pt9B_
not modelled 95.6 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:nad(p) transhydrogenase, mitochondrial;
PDBTitle: crystal structure analysis of the diii component of transhydrogenase2 with a thio-nicotinamide nucleotide analogue

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