Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AFG8
DateThu Jan 5 11:26:11 GMT 2012
Unique Job IDd3da3f34fd0d5c0c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2g28A_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate dehydrogenase e1 component;
PDBTitle: e. coli pyruvate dehydrogenase h407a variant2 phosphonolactylthiamin diphosphate complex
Confidence and coverage
Confidence:100.0% Coverage: 90%
801 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  MSERFPNDVDPIETRDWLQAIESVIREEGVERAQYLIDQLLAEARKGGVNVAAGTGISNY
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Disorder  ???????
?




































??????????????
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   .........70.........80.........90.........100.........110.........120
Sequence  INTIPVEEQPEYPGNLELERRIRSAIRWNAIMTVLRASKKDLELGGHMASFQSSATIYDV
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Disorder  ??????????????






















???????















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   .........130.........140.........150.........160.........170.........180
Sequence  CFNHFFRARNEQDGGDLVYFQGHISPGVYARAFLEGRLTQEQLDNFRQEVHGNGLSSYPH
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??????




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   .........190.........200.........210.........220.........230.........240
Sequence  PKLMPEFWQFPTVSMGLGPIGAIYQAKFLKYLEHRGLKDTSKQTVYAFLGDGEMDEPESK
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???????




















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   .........250.........260.........270.........280.........290.........300
Sequence  GAITIATREKLDNLVFVINCNLQRLDGPVTGNGKIINELEGIFEGAGWNVIKVMWGSRWD
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   .........310.........320.........330.........340.........350.........360
Sequence  ELLRKDTSGKLIQLMNETVDGDYQTFKSKDGAYVREHFFGKYPETAALVADWTDEQIWAL
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???
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   .........370.........380.........390.........400.........410.........420
Sequence  NRGGHDPKKIYAAFKKAQETKGKATVILAHTIKGYGMGDAAEGKNIAHQVKKMNMDGVRH
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Disorder 
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   .........430.........440.........450.........460.........470.........480
Sequence  IRDRFNVPVSDADIEKLPYITFPEGSEEHTYLHAQRQKLHGYLPSRQPNFTEKLELPSLQ
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Disorder 









??
































?

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   .........490.........500.........510.........520.........530.........540
Sequence  DFGALLEEQSKEISTTIAFVRALNVMLKNKSIKDRLVPIIADEARTFGMEGLFRQIGIYS
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Disorder 
????

???????















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?



?
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??
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   .........550.........560.........570.........580.........590.........600
Sequence  PNGQQYTPQDREQVAYYKEDEKGQILQEGINELGAGCSWLAAATSYSTNNLPMIPFYIYY
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   .........610.........620.........630.........640.........650.........660
Sequence  SMFGFQRIGDLCWAAGDQQARGFLIGGTSGRTTLNGEGLQHEDGHSHIQSLTIPNCISYD
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   .........670.........680.........690.........700.........710.........720
Sequence  PAYAYEVAVIMHDGLERMYGEKQENVYYYITTLNENYHMPAMPEGAEEGIRKGIYKLETI
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   .........730.........740.........750.........760.........770.........780
Sequence  EGSKGKVQLLGSGSILRHVREAAEILAKDYGVGSDVYSVTSFTELARDGQDCERWNMLHP
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   .........790.........800.........810.........820.........830.........840
Sequence  LETPRVPYIAQVMNDAPAVASTDYMKLFAEQVRTYVPADDYRVLGTDGFGRSDSRENLRH
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   .........850.........860.........870.........880.......
Sequence  HFEVDASYVVVAALGELAKRGEIDKKVVADAIAKFNIDADKVNPRLA
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????

???????
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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 2g28 chain A

3D model

Region: 57 - 887
Aligned: 801
Modelled: 801
Confidence: 100.0%
Identity: 100%
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate dehydrogenase e1 component;
PDBTitle: e. coli pyruvate dehydrogenase h407a variant2 phosphonolactylthiamin diphosphate complex

Phyre2

PDB 3ahh chain A

3D model

Region: 65 - 886
Aligned: 730
Modelled: 766
Confidence: 100.0%
Identity: 16%
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

Phyre2

PDB 1r9j chain B

3D model

Region: 80 - 867
Aligned: 644
Modelled: 684
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: transketolase from leishmania mexicana

Phyre2

PDB 2r8p chain A

3D model

Region: 79 - 857
Aligned: 642
Modelled: 685
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: A: PDB Molecule:transketolase 1;
PDBTitle: transketolase from e. coli in complex with substrate d-2 fructose-6-phosphate

Phyre2

PDB 3hyl chain B

3D model

Region: 78 - 857
Aligned: 646
Modelled: 662
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of transketolase from bacillus anthracis

Phyre2

PDB 3kom chain B

3D model

Region: 78 - 857
Aligned: 630
Modelled: 669
Confidence: 100.0%
Identity: 22%
PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of apo transketolase from francisella tularensis

Phyre2

PDB 3m7i chain A

3D model

Region: 75 - 855
Aligned: 625
Modelled: 663
Confidence: 100.0%
Identity: 21%
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

Phyre2

PDB 1tkc chain A

3D model

Region: 77 - 871
Aligned: 657
Modelled: 694
Confidence: 100.0%
Identity: 22%
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

Phyre2

PDB 1itz chain C

3D model

Region: 77 - 853
Aligned: 640
Modelled: 673
Confidence: 100.0%
Identity: 22%
PDB header:transferase
Chain: C: PDB Molecule:transketolase;
PDBTitle: maize transketolase in complex with tpp

Phyre2

PDB 2e6k chain B

3D model

Region: 77 - 857
Aligned: 636
Modelled: 674
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: x-ray structure of thermus thermopilus hb8 tt0505

Phyre2

PDB 3uk1 chain A

3D model

Region: 78 - 858
Aligned: 627
Modelled: 657
Confidence: 100.0%
Identity: 25%
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

Phyre2

PDB 3mos chain A

3D model

Region: 80 - 853
Aligned: 597
Modelled: 617
Confidence: 100.0%
Identity: 22%
PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: the structure of human transketolase

Phyre2

PDB 2iea chain A domain 2

3D model

Region: 57 - 470
Aligned: 401
Modelled: 414
Confidence: 100.0%
Identity: 100%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: TK-like PP module

Phyre2

PDB 2o1s chain C

3D model

Region: 80 - 858
Aligned: 508
Modelled: 554
Confidence: 100.0%
Identity: 19%
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

Phyre2

PDB 2o1x chain A

3D model

Region: 53 - 860
Aligned: 575
Modelled: 641
Confidence: 100.0%
Identity: 19%
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

Phyre2

PDB 1itz chain A domain 1

3D model

Region: 75 - 474
Aligned: 318
Modelled: 331
Confidence: 100.0%
Identity: 25%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: TK-like PP module

Phyre2

PDB 1r9j chain A domain 2

3D model

Region: 80 - 479
Aligned: 317
Modelled: 325
Confidence: 100.0%
Identity: 23%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: TK-like PP module

Phyre2

PDB 1gpu chain A domain 1

3D model

Region: 77 - 475
Aligned: 315
Modelled: 330
Confidence: 100.0%
Identity: 26%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: TK-like PP module

Phyre2

PDB 2r8o chain A domain 2

3D model

Region: 80 - 474
Aligned: 314
Modelled: 327
Confidence: 100.0%
Identity: 26%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: TK-like PP module

Phyre2

PDB 2iea chain A domain 1

3D model

Region: 472 - 701
Aligned: 213
Modelled: 213
Confidence: 100.0%
Identity: 100%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: TK-like Pyr module

Phyre2

PDB 3h87 chain D

3D model

Region: 16 - 51
Aligned: 36
Modelled: 36
Confidence: 69.1%
Identity: 25%
PDB header:toxin/antitoxin
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis

Phyre2
1

c2g28A_
2

c3ahhA_
3

c1r9jB_
4

c2r8pA_
5

c3hylB_
6

c3komB_
7

c3m7iA_
8

c1tkcA_
9

c1itzC_
10

c2e6kB_
11

c3uk1A_
12

c3mosA_
13

d2ieaa2
14

c2o1sC_
15

c2o1xA_
16

d1itza1
17

d1r9ja2
18

d1gpua1
19

d2r8oa2
20

d2ieaa1
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c3h87D_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2g28A_



100.0 100 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate dehydrogenase e1 component;
PDBTitle: e. coli pyruvate dehydrogenase h407a variant2 phosphonolactylthiamin diphosphate complex
2c3ahhA_



100.0 16 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
3c1r9jB_



100.0 21 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: transketolase from leishmania mexicana
4c2r8pA_



100.0 24 PDB header:transferase
Chain: A: PDB Molecule:transketolase 1;
PDBTitle: transketolase from e. coli in complex with substrate d-2 fructose-6-phosphate
5c3hylB_



100.0 21 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of transketolase from bacillus anthracis
6c3komB_



100.0 22 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of apo transketolase from francisella tularensis
7c3m7iA_



100.0 21 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
8c1tkcA_



100.0 22 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
9c1itzC_



100.0 22 PDB header:transferase
Chain: C: PDB Molecule:transketolase;
PDBTitle: maize transketolase in complex with tpp
10c2e6kB_



100.0 24 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: x-ray structure of thermus thermopilus hb8 tt0505
11c3uk1A_



100.0 25 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
12c3mosA_



100.0 22 PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: the structure of human transketolase
13d2ieaa2



100.0 100 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
14c2o1sC_



100.0 19 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
15c2o1xA_



100.0 19 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
16d1itza1



100.0 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
17d1r9ja2



100.0 23 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
18d1gpua1



100.0 26 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
19d2r8oa2



100.0 26 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like PP module
20d2ieaa1



100.0 100 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
21d2ieaa3



not modelled 100.0 100 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Transketolase C-terminal domain-like
22c1um9D_



not modelled 100.0 13 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
23d1gpua2



not modelled 100.0 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
24c3dufD_



not modelled 100.0 12 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
25d1r9ja1



not modelled 100.0 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
26d1itza2



not modelled 100.0 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
27c1olsB_



not modelled 100.0 13 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
28d2r8oa1



not modelled 100.0 19 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
29c1ni4D_



not modelled 100.0 13 PDB header:oxidoreductase
Chain: D: PDB Molecule:pyruvate dehydrogenase e1 component: beta
PDBTitle: human pyruvate dehydrogenase
30c2bp7F_



not modelled 100.0 14 PDB header:oxidoreductase
Chain: F: PDB Molecule:2-oxoisovalerate dehydrogenase beta subunit;
PDBTitle: new crystal form of the pseudomonas putida branched-chain2 dehydrogenase (e1)
31c1ik6A_



not modelled 100.0 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
32d2bfda1



not modelled 99.9 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
33d1w85a_



not modelled 99.9 20 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
34d1itza3



not modelled 99.9 24 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Transketolase C-terminal domain-like
35d1r9ja3



not modelled 99.9 18 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Transketolase C-terminal domain-like
36d2ozla1



not modelled 99.9 16 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
37d1umda_



not modelled 99.9 18 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
38d1umdb1



not modelled 99.9 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
39d2r8oa3



not modelled 99.9 24 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Transketolase C-terminal domain-like
40d1gpua3



not modelled 99.9 21 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Transketolase C-terminal domain-like
41d1w85b1



not modelled 99.9 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
42d2ozlb1



not modelled 99.8 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
43d1qs0a_



not modelled 99.8 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase PP module
44d2bfdb1



not modelled 99.8 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
45d1qs0b1



not modelled 99.7 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
46c2yicC_



not modelled 99.7 15 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)
47d1ik6a1



not modelled 99.7 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
48d1w85b2



not modelled 99.5 10 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
49d1q6za3



not modelled 99.4 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
50d1umdb2



not modelled 99.3 18 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
51d1t9ba3



not modelled 99.3 21 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
52d2ozlb2



not modelled 99.3 13 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
53c2jgdA_



not modelled 99.3 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-oxoglutarate dehydrogenase e1 component;
PDBTitle: e. coli 2-oxoglutarate dehydrogenase (e1o)
54d2djia3



not modelled 99.3 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
55d2bfdb2



not modelled 99.3 11 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
56d2ez9a3



not modelled 99.3 16 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
57d1jsca3



not modelled 99.2 22 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
58c1powA_



not modelled 99.2 15 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
59d2ihta3



not modelled 99.2 23 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
60c2djiA_



not modelled 99.2 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: crystal structure of pyruvate oxidase from aerococcus2 viridans containing fad
61c2xt6B_



not modelled 99.2 14 PDB header:lyase
Chain: B: PDB Molecule:2-oxoglutarate decarboxylase;
PDBTitle: crystal structure of mycobacterium smegmatis alpha-ketoglutarate2 decarboxylase homodimer (orthorhombic form)
62d1ozha3



not modelled 99.2 21 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
63d1ybha3



not modelled 99.2 21 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
64d2ji7a3



not modelled 99.1 24 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
65c2nxwB_



not modelled 99.0 25 PDB header:lyase
Chain: B: PDB Molecule:phenyl-3-pyruvate decarboxylase;
PDBTitle: crystal structure of phenylpyruvate decarboxylase of azospirillum2 brasilense
66d1pvda3



not modelled 99.0 22 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
67c1jscA_



not modelled 99.0 19 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
68c1t9dB_



not modelled 99.0 20 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
69c1upaC_



not modelled 99.0 24 PDB header:synthase
Chain: C: PDB Molecule:carboxyethylarginine synthase;
PDBTitle: carboxyethylarginine synthase from streptomyces2 clavuligerus (semet structure)
70c2ag1A_



not modelled 99.0 25 PDB header:lyase
Chain: A: PDB Molecule:benzaldehyde lyase;
PDBTitle: crystal structure of benzaldehyde lyase (bal)- semet
71c2v3wC_



not modelled 99.0 23 PDB header:lyase
Chain: C: PDB Molecule:benzoylformate decarboxylase;
PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida
72d1ovma3



not modelled 98.9 18 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
73c3eyaE_



not modelled 98.9 23 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
74c2pgnA_



not modelled 98.9 22 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
75d1qs0b2



not modelled 98.9 16 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
76c1yi1A_



not modelled 98.9 21 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
77c2q27B_



not modelled 98.9 24 PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: crystal structure of oxalyl-coa decarboxylase from escherichia coli
78c2vbiF_



not modelled 98.9 24 PDB header:lyase
Chain: F: PDB Molecule:pyruvate decarboxylase;
PDBTitle: holostructure of pyruvate decarboxylase from acetobacter2 pasteurianus
79c2panF_



not modelled 98.8 21 PDB header:lyase
Chain: F: PDB Molecule:glyoxylate carboligase;
PDBTitle: crystal structure of e. coli glyoxylate carboligase
80c1ozhD_



not modelled 98.8 21 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.
81c1zpdA_



not modelled 98.8 21 PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis
82c2w93A_



not modelled 98.8 24 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
83c3lq1A_



not modelled 98.7 18 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
84c1ovmC_



not modelled 98.7 17 PDB header:lyase
Chain: C: PDB Molecule:indole-3-pyruvate decarboxylase;
PDBTitle: crystal structure of indolepyruvate decarboxylase from2 enterobacter cloacae
85c2vbgB_



not modelled 98.7 28 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
86d1zpda3



not modelled 98.7 23 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
87c2ji6B_



not modelled 98.7 23 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
88c2jlaD_



not modelled 98.7 18 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
89c2x7jA_



not modelled 98.5 16 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
90d1ik6a2



not modelled 98.5 13 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
91c3ju3A_



not modelled 98.1 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:probable 2-oxoacid ferredoxin oxidoreductase, alpha chain;
PDBTitle: crystal structure of alpha chain of probable 2-oxoacid ferredoxin2 oxidoreductase from thermoplasma acidophilum
92c2c3yA_



not modelled 97.8 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase;
PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus
93d2c42a2



not modelled 97.7 23 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:PFOR PP module
94d2c42a3



not modelled 97.3 13 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
95d1q6za2



not modelled 95.0 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
96c3a9rA_



not modelled 94.0 18 PDB header:isomerase
Chain: A: PDB Molecule:d-arabinose isomerase;
PDBTitle: x-ray structures of bacillus pallidus d-arabinose2 isomerasecomplex with (4r)-2-methylpentane-2,4-diol
97d1ybha2



not modelled 92.1 12 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
98d2ihta2



not modelled 90.2 7 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
99d1t9ba2



not modelled 87.0 11 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
100c1fuiB_



not modelled 83.7 15 PDB header:isomerase
Chain: B: PDB Molecule:l-fucose isomerase;
PDBTitle: l-fucose isomerase from escherichia coli
101d2ez9a2



not modelled 79.2 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
102d2c42a1



not modelled 79.2 9 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:PFOR Pyr module
103d1vm0a_



not modelled 77.5 28 Fold:IF3-like
Superfamily:AlbA-like
Family:Hypothetical protein At2g34160
104d1ozha2



not modelled 75.9 7 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
105c2q3vB_



not modelled 75.6 24 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:protein at2g34160;
PDBTitle: ensemble refinement of the protein crystal structure of gene product2 from arabidopsis thaliana at2g34160
106c2k2eA_



not modelled 74.1 24 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein bp2786;
PDBTitle: solution nmr structure of bordetella pertussis protein2 bp2786, a mth938-like domain. northeast structural3 genomics consortium target ber31
107c2gm2A_



not modelled 73.3 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: nmr structure of xanthomonas campestris xcc1710: northeast2 structural genomics consortium target xcr35
108c3o8nA_



not modelled 72.9 16 PDB header:transferase
Chain: A: PDB Molecule:6-phosphofructokinase, muscle type;
PDBTitle: structure of phosphofructokinase from rabbit skeletal muscle
109c2h9uA_



not modelled 72.8 18 PDB header:dna binding protein
Chain: A: PDB Molecule:dna/rna-binding protein alba 2;
PDBTitle: crystal structure of the archaea specific dna binding protein
110d2q4qa1



not modelled 69.6 26 Fold:MTH938-like
Superfamily:MTH938-like
Family:MTH938-like
111c3h87D_



69.1 25 PDB header:toxin/antitoxin
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis
112d2fi9a1



not modelled 69.0 28 Fold:MTH938-like
Superfamily:MTH938-like
Family:MTH938-like
113c2oaq1_



not modelled 68.5 19 PDB header:hydrolase
Chain: 1: PDB Molecule:type ii secretion system protein;
PDBTitle: crystal structure of the archaeal secretion atpase gspe in complex2 with phosphate
114d1fuia2



not modelled 63.3 16 Fold:FucI/AraA N-terminal and middle domains
Superfamily:FucI/AraA N-terminal and middle domains
Family:L-fucose isomerase, N-terminal and second domains
115c3l3bA_



not modelled 62.1 25 PDB header:biosynthetic protein
Chain: A: PDB Molecule:es1 family protein;
PDBTitle: crystal structure of isoprenoid biosynthesis protein with2 amidotransferase-like domain from ehrlichia chaffeensis at 1.90a3 resolution
116c3lp6D_



not modelled 60.5 29 PDB header:lyase
Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit;
PDBTitle: crystal structure of rv3275c-e60a from mycobacterium tuberculosis at2 1.7a resolution
117c3opyG_



not modelled 57.0 12 PDB header:transferase
Chain: G: PDB Molecule:6-phosphofructo-1-kinase alpha-subunit;
PDBTitle: crystal structure of pichia pastoris phosphofructokinase in the t-2 state
118c3o8oC_



not modelled 56.7 11 PDB header:transferase
Chain: C: PDB Molecule:6-phosphofructokinase subunit alpha;
PDBTitle: structure of phosphofructokinase from saccharomyces cerevisiae
119c3c3jA_



not modelled 54.3 18 PDB header:isomerase
Chain: A: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase;
PDBTitle: crystal structure of tagatose-6-phosphate ketose/aldose isomerase from2 escherichia coli
120d1pfka_



not modelled 53.4 19 Fold:Phosphofructokinase
Superfamily:Phosphofructokinase
Family:Phosphofructokinase

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