Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP52647
DateThu Jan 5 12:05:59 GMT 2012
Unique Job IDb53f627ed870c447

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2c3yA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase;
PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus
Confidence and coverage
Confidence:100.0% Coverage: 98%
1153 residues ( 98% 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  MITIDGNGAVASVAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDTPRVVEMQSE
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Disorder  ?

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   .........70.........80.........90.........100.........110.........120
Sequence  AGAIATVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGELTPFVLHVAARTVATHALSIF
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??




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   .........130.........140.........150.........160.........170.........180
Sequence  GDHSDVMAVRQTGCAMLCAANVQEAQDFALISQIATLKSRVPFIHFFDGFRTSHEINKIV
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   .........190.........200.........210.........220.........230.........240
Sequence  PLADDTILDLMPQVEIDAHRARALNPEHPVIRGTSANPDTYFQSREATNPWYNAVYDHVE
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?
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   .........250.........260.........270.........280.........290.........300
Sequence  QAMNDFSAATGRQYQPFEYYGHPQAERVIILMGSAIGTCEEVVDELLTRGEKVGVLKVRL
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   .........310.........320.........330.........340.........350.........360
Sequence  YRPFSAKHLLQALPGSVRSVAVLDRTKEPGAQAEPLYLDVMTALAEAFNNGERETLPRVI
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???

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   .........370.........380.........390.........400.........410.........420
Sequence  GGRYGLSSKEFGPDCVLAVFAELNAAKPKARFTVGIYDDVTNLSLPLPENTLPNSAKLEA
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   .........430.........440.........450.........460.........470.........480
Sequence  LFYGLGSDGSVSATKNNIKIIGNSTPWYAQGYFVYDSKKAGGLTVSHLRVSEQPIRSAYL
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   .........490.........500.........510.........520.........530.........540
Sequence  ISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSADEVWSRLPQEVQAVLNQKKARF
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   .........550.........560.........570.........580.........590.........600
Sequence  YVINAAKIARECGLAARINTVMQMAFFHLTQILPGDSALAELQGAIAKSYSSKGQDLVER
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   .........610.........620.........630.........640.........650.........660
Sequence  NWQALALARESVEEVPLQPVNPHSANRPPVVSDAAPDFVKTVTAAMLAGLGDALPVSALP
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   .........670.........680.........690.........700.........710.........720
Sequence  PDGTWPMGTTRWEKRNIAEEIPIWKEELCTQCNHCVAACPHSAIRAKVVPPEAMENAPAS
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??

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?????
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   .........730.........740.........750.........760.........770.........780
Sequence  LHSLDVKSRDMRGQKYVLQVAPEDCTGCNLCVEVCPAKDRQNPEIKAINMMSRLEHVEEE
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Disorder  ?
???????
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???????????
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   .........790.........800.........810.........820.........830.........840
Sequence  KINYDFFLNLPEIDRSKLERIDIRTSQLITPLFEYSGACSGCGETPYIKLLTQLYGDRML
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????
???

???
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   .........850.........860.........870.........880.........890.........900
Sequence  IANATGCSSIYGGNLPSTPYTTDANGRGPAWANSLFEDNAEFGLGFRLTVDQHRVRVLRL
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?
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   .........910.........920.........930.........940.........950.........960
Sequence  LDQFADKIPAELLTALKSDATPEVRREQVAALRQQLNDVAEAHELLRDADALVEKSIWLI
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   .........970.........980.........990.........1000.........1010.........1020
Sequence  GGDGWAYDIGFGGLDHVLSLTENVNILVLDTQCYSNTGGQASKATPLGAVTKFGEHGKRK
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???????

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   .........1030.........1040.........1050.........1060.........1070.........1080
Sequence  ARKDLGVSMMMYGHVYVAQISLGAQLNQTVKAIQEAEAYPGPSLIIAYSPCEEHGYDLAL
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   .........1090.........1100.........1110.........1120.........1130.........1140
Sequence  SHDQMRQLTATGFWPLYRFDPRRADEGKLPLALDSRPPSEAPEETLLHEQRFRRLNSQQP
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??????????


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?
??

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   .........1150.........1160.........1170....
Sequence  EVAEQLWKDAAADLQKRYDFLAQMAGKAEKSNTD
Secondary structure 





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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 2c3y chain A

3D model

Region: 1 - 1167
Aligned: 1153
Modelled: 1167
Confidence: 100.0%
Identity: 47%
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase;
PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus

Phyre2

PDB 2c42 chain A domain 2

3D model

Region: 793 - 1167
Aligned: 375
Modelled: 375
Confidence: 100.0%
Identity: 46%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: PFOR PP module

Phyre2

PDB 2c42 chain A domain 1

3D model

Region: 1 - 254
Aligned: 254
Modelled: 254
Confidence: 100.0%
Identity: 59%
Fold: Thiamin diphosphate-binding fold (THDP-binding)
Superfamily: Thiamin diphosphate-binding fold (THDP-binding)
Family: PFOR Pyr module

Phyre2

PDB 2c42 chain A domain 4

3D model

Region: 416 - 668
Aligned: 252
Modelled: 253
Confidence: 100.0%
Identity: 42%
Fold: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Superfamily: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Family: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III

Phyre2

PDB 1yd7 chain A

3D model

Region: 2 - 192
Aligned: 158
Modelled: 170
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase
Chain: A: PDB Molecule:2-keto acid:ferredoxin oxidoreductase subunit
PDBTitle: conserved hypothetical protein pfu-1647980-001 from2 pyrococcus furiosus

Phyre2

PDB 2c42 chain A domain 3

3D model

Region: 255 - 412
Aligned: 152
Modelled: 158
Confidence: 100.0%
Identity: 51%
Fold: TK C-terminal domain-like
Superfamily: TK C-terminal domain-like
Family: Pyruvate-ferredoxin oxidoreductase, PFOR, domain II

Phyre2

PDB 2dji chain A

3D model

Region: 4 - 1137
Aligned: 568
Modelled: 614
Confidence: 99.9%
Identity: 18%
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: crystal structure of pyruvate oxidase from aerococcus2 viridans containing fad

Phyre2

PDB 1t9d chain B

3D model

Region: 1 - 618
Aligned: 503
Modelled: 533
Confidence: 99.9%
Identity: 11%
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 1jsc chain A

3D model

Region: 1 - 599
Aligned: 496
Modelled: 518
Confidence: 99.9%
Identity: 13%
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 2c42 chain A domain 5

3D model

Region: 669 - 791
Aligned: 117
Modelled: 123
Confidence: 99.9%
Identity: 36%
Fold: Ferredoxin-like
Superfamily: 4Fe-4S ferredoxins
Family: Ferredoxin domains from multidomain proteins

Phyre2

PDB 3eya chain E

3D model

Region: 4 - 599
Aligned: 489
Modelled: 513
Confidence: 99.8%
Identity: 11%
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 2ag1 chain A

3D model

Region: 4 - 618
Aligned: 488
Modelled: 510
Confidence: 99.8%
Identity: 13%
PDB header:lyase
Chain: A: PDB Molecule:benzaldehyde lyase;
PDBTitle: crystal structure of benzaldehyde lyase (bal)- semet

Phyre2

PDB 2w93 chain A

3D model

Region: 4 - 611
Aligned: 477
Modelled: 490
Confidence: 99.8%
Identity: 10%
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

PDB 2ji6 chain B

3D model

Region: 1 - 618
Aligned: 505
Modelled: 537
Confidence: 99.8%
Identity: 11%
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: 3 - 599
Aligned: 495
Modelled: 522
Confidence: 99.8%
Identity: 14%
PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis

Phyre2

PDB 2nxw chain B

3D model

Region: 4 - 644
Aligned: 507
Modelled: 546
Confidence: 99.8%
Identity: 12%
PDB header:lyase
Chain: B: PDB Molecule:phenyl-3-pyruvate decarboxylase;
PDBTitle: crystal structure of phenylpyruvate decarboxylase of azospirillum2 brasilense

Phyre2

PDB 2pan chain F

3D model

Region: 4 - 618
Aligned: 524
Modelled: 542
Confidence: 99.8%
Identity: 10%
PDB header:lyase
Chain: F: PDB Molecule:glyoxylate carboligase;
PDBTitle: crystal structure of e. coli glyoxylate carboligase

Phyre2

PDB 1yi1 chain A

3D model

Region: 4 - 629
Aligned: 534
Modelled: 551
Confidence: 99.8%
Identity: 12%
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 1ozh chain D

3D model

Region: 3 - 618
Aligned: 493
Modelled: 535
Confidence: 99.8%
Identity: 12%
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 2pgn chain A

3D model

Region: 5 - 611
Aligned: 497
Modelled: 530
Confidence: 99.7%
Identity: 14%
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
1

c2c3yA_
2

d2c42a2
3

d2c42a1
4

d2c42a4
5

c1yd7A_
6

d2c42a3
7

c2djiA_
8

c1t9dB_
9

c1jscA_
10

d2c42a5
11

c3eyaE_
12

c2ag1A_
13

c2w93A_
14

c2ji6B_
15

c1zpdA_
16

c2nxwB_
17

c2panF_
18

c1yi1A_
19

c1ozhD_
20

c2pgnA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2c3yA_



100.0 47 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase;
PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus
2d2c42a2



100.0 46 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:PFOR PP module
3d2c42a1



100.0 59 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:PFOR Pyr module
4d2c42a4



100.0 42 Fold:Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Superfamily:Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
5c1yd7A_



100.0 28 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-keto acid:ferredoxin oxidoreductase subunit
PDBTitle: conserved hypothetical protein pfu-1647980-001 from2 pyrococcus furiosus
6d2c42a3



100.0 51 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
7c2djiA_



99.9 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: crystal structure of pyruvate oxidase from aerococcus2 viridans containing fad
8c1t9dB_



99.9 11 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
9c1jscA_



99.9 13 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
10d2c42a5



99.9 36 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
11c3eyaE_



99.8 11 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
12c2ag1A_



99.8 13 PDB header:lyase
Chain: A: PDB Molecule:benzaldehyde lyase;
PDBTitle: crystal structure of benzaldehyde lyase (bal)- semet
13c2w93A_



99.8 10 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
14c2ji6B_



99.8 11 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
15c1zpdA_



99.8 14 PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis
16c2nxwB_



99.8 12 PDB header:lyase
Chain: B: PDB Molecule:phenyl-3-pyruvate decarboxylase;
PDBTitle: crystal structure of phenylpyruvate decarboxylase of azospirillum2 brasilense
17c2panF_



99.8 10 PDB header:lyase
Chain: F: PDB Molecule:glyoxylate carboligase;
PDBTitle: crystal structure of e. coli glyoxylate carboligase
18c1yi1A_



99.8 12 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
19c1ozhD_



99.8 12 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.
20c2pgnA_



99.7 14 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
21c2q27B_



not modelled 99.7 11 PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: crystal structure of oxalyl-coa decarboxylase from escherichia coli
22c1upaC_



not modelled 99.7 11 PDB header:synthase
Chain: C: PDB Molecule:carboxyethylarginine synthase;
PDBTitle: carboxyethylarginine synthase from streptomyces2 clavuligerus (semet structure)
23c1powA_



not modelled 99.7 10 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
24c2raaA_



not modelled 99.7 23 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate synthase subunit porc;
PDBTitle: crystal structure of pyruvate oxidoreductase subunit porc (ec 1.2.7.1)2 (tm0015) from thermotoga maritima at 2.12 a resolution
25c1ovmC_



not modelled 99.7 13 PDB header:lyase
Chain: C: PDB Molecule:indole-3-pyruvate decarboxylase;
PDBTitle: crystal structure of indolepyruvate decarboxylase from2 enterobacter cloacae
26c2x7jA_



not modelled 99.7 10 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
27c2v3wC_



not modelled 99.7 11 PDB header:lyase
Chain: C: PDB Molecule:benzoylformate decarboxylase;
PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida
28c2vbiF_



not modelled 99.7 14 PDB header:lyase
Chain: F: PDB Molecule:pyruvate decarboxylase;
PDBTitle: holostructure of pyruvate decarboxylase from acetobacter2 pasteurianus
29c2vbgB_



not modelled 99.6 13 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
30c3g2eA_



not modelled 99.6 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:oorc subunit of 2-oxoglutarate:acceptor oxidoreductase;
PDBTitle: structure of putative oorc subunit of 2-oxoglutarate:acceptor2 oxidoreductase from campylobacter jejuni
31d2ez9a2



not modelled 99.6 9 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
32c2bp7F_



not modelled 99.6 15 PDB header:oxidoreductase
Chain: F: PDB Molecule:2-oxoisovalerate dehydrogenase beta subunit;
PDBTitle: new crystal form of the pseudomonas putida branched-chain2 dehydrogenase (e1)
33d1t9ba2



not modelled 99.6 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
34d1ybha3



not modelled 99.5 20 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
35c3on3B_



not modelled 99.5 23 PDB header:oxidoreductase
Chain: B: PDB Molecule:keto/oxoacid ferredoxin oxidoreductase, gamma subunit;
PDBTitle: the crystal structure of keto/oxoacid ferredoxin oxidoreductase, gamma2 subunit from geobacter sulfurreducens pca
36c3lq1A_



not modelled 99.5 13 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
37c1ni4D_



not modelled 99.5 14 PDB header:oxidoreductase
Chain: D: PDB Molecule:pyruvate dehydrogenase e1 component: beta
PDBTitle: human pyruvate dehydrogenase
38c3ju3A_



not modelled 99.5 17 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
39c1um9D_



not modelled 99.5 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
40c1olsB_



not modelled 99.5 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
41d1ybha2



not modelled 99.4 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
42c3mosA_



not modelled 99.4 13 PDB header:transferase
Chain: A: PDB Molecule:transketolase;
PDBTitle: the structure of human transketolase
43c3dufD_



not modelled 99.4 13 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
44d2ji7a2



not modelled 99.4 11 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
45c2jlaD_



not modelled 99.4 12 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
46d2djia2



not modelled 99.4 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
47d1pvda2



not modelled 99.4 12 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
48d2ez9a3



not modelled 99.4 13 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
49d1gtea5



not modelled 99.4 28 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
50c1gthD_



not modelled 99.4 28 PDB header:oxidoreductase
Chain: D: PDB Molecule:dihydropyrimidine dehydrogenase;
PDBTitle: dihydropyrimidine dehydrogenase (dpd) from pig, ternary2 complex with nadph and 5-iodouracil
51d2ihta3



not modelled 99.3 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
52c2o1xA_



not modelled 99.2 16 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
53d1t9ba3



not modelled 99.2 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
54d1ozha3



not modelled 99.2 16 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
55d2fug91



not modelled 99.2 22 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
56c2fugG_



not modelled 99.2 22 PDB header:oxidoreductase
Chain: G: PDB Molecule:nadh-quinone oxidoreductase chain 9;
PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus
57c1tkcA_



not modelled 99.2 13 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
58d2djia3



not modelled 99.2 12 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
59c2o1sC_



not modelled 99.2 12 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
60c2gmhA_



not modelled 99.2 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:electron transfer flavoprotein-ubiquinone
PDBTitle: structure of porcine electron transfer flavoprotein-2 ubiquinone oxidoreductase in complexed with ubiquinone
61d1xera_



not modelled 99.1 23 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Archaeal ferredoxins
62c1ik6A_



not modelled 99.1 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate dehydrogenase;
PDBTitle: 3d structure of the e1beta subunit of pyruvate2 dehydrogenase from the archeon pyrobaculum aerophilum
63c3m7iA_



not modelled 99.1 15 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
64d1hfel2



not modelled 99.0 23 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
65c2v4jE_



not modelled 99.0 17 PDB header:oxidoreductase
Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit
PDBTitle: the crystal structure of desulfovibrio vulgaris2 dissimilatory sulfite reductase bound to dsrc provides3 novel insights into the mechanism of sulfate respiration
66d1jb0c_



not modelled 99.0 28 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:7-Fe ferredoxin
67c2e6kB_



not modelled 99.0 15 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: x-ray structure of thermus thermopilus hb8 tt0505
68c2r8pA_



not modelled 99.0 15 PDB header:transferase
Chain: A: PDB Molecule:transketolase 1;
PDBTitle: transketolase from e. coli in complex with substrate d-2 fructose-6-phosphate
69c1itzC_



not modelled 99.0 18 PDB header:transferase
Chain: C: PDB Molecule:transketolase;
PDBTitle: maize transketolase in complex with tpp
70d1jsca3



not modelled 99.0 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
71c3komB_



not modelled 99.0 15 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of apo transketolase from francisella tularensis
72d3c8ya3



not modelled 99.0 18 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
73c1r9jB_



not modelled 98.9 14 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: transketolase from leishmania mexicana
74d1h98a_



not modelled 98.9 25 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:7-Fe ferredoxin
75d7fd1a_



not modelled 98.9 23 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:7-Fe ferredoxin
76d1ovma3



not modelled 98.9 16 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
77c3gyxJ_



not modelled 98.9 23 PDB header:oxidoreductase
Chain: J: PDB Molecule:adenylylsulfate reductase;
PDBTitle: crystal structure of adenylylsulfate reductase from2 desulfovibrio gigas
78d1zpda2



not modelled 98.9 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
79d1jnrb_



not modelled 98.9 24 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
80d1ozha2



not modelled 98.9 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
81c1gx7A_



not modelled 98.9 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:periplasmic [fe] hydrogenase large subunit;
PDBTitle: best model of the electron transfer complex between2 cytochrome c3 and [fe]-hydrogenase
82d1q6za3



not modelled 98.9 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
83c1hfeL_



not modelled 98.9 23 PDB header:hydrogenase
Chain: L: PDB Molecule:protein (fe-only hydrogenase (e.c.1.18.99.1)
PDBTitle: 1.6 a resolution structure of the fe-only hydrogenase from2 desulfovibrio desulfuricans
84d1pvda3



not modelled 98.8 17 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
85d1bc6a_



not modelled 98.8 28 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:7-Fe ferredoxin
86d2ji7a3



not modelled 98.8 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
87c3uk1A_



not modelled 98.8 18 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
88d1umdb2



not modelled 98.7 14 Fold:TK C-terminal domain-like
Superfamily:TK C-terminal domain-like
Family:Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
89d1dura_



not modelled 98.7 23 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Short-chain ferredoxins
90d2fdna_



not modelled 98.7 26 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Short-chain ferredoxins
91c2vpyB_



not modelled 98.7 22 PDB header:oxidoreductase
Chain: B: PDB Molecule:nrfc protein;
PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp)
92d2fug34



not modelled 98.7 14 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
93d1blua_



not modelled 98.7 22 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Short-chain ferredoxins
94d1vjwa_



not modelled 98.7 16 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Single 4Fe-4S cluster ferredoxin
95c2xt6B_



not modelled 98.7 14 PDB header:lyase
Chain: B: PDB Molecule:2-oxoglutarate decarboxylase;
PDBTitle: crystal structure of mycobacterium smegmatis alpha-ketoglutarate2 decarboxylase homodimer (orthorhombic form)
96d1q6za2



not modelled 98.7 12 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
97d2ozlb2



not modelled 98.7 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
98c3hylB_



not modelled 98.7 16 PDB header:transferase
Chain: B: PDB Molecule:transketolase;
PDBTitle: crystal structure of transketolase from bacillus anthracis
99c3c7bE_



not modelled 98.7 32 PDB header:oxidoreductase
Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit beta;
PDBTitle: structure of the dissimilatory sulfite reductase from archaeoglobus2 fulgidus
100d1vlfn2



not modelled 98.7 17 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
101c1kqfB_



not modelled 98.7 32 PDB header:oxidoreductase
Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur
PDBTitle: formate dehydrogenase n from e. coli
102c2zvsB_



not modelled 98.7 23 PDB header:electron transport
Chain: B: PDB Molecule:uncharacterized ferredoxin-like protein yfhl;
PDBTitle: crystal structure of the 2[4fe-4s] ferredoxin from escherichia coli
103d1iqza_



not modelled 98.7 15 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Single 4Fe-4S cluster ferredoxin
104d1y5ib1



not modelled 98.6 31 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
105d2ihta2



not modelled 98.6 11 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
106d3c7bb1



not modelled 98.6 30 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
107d1fcaa_



not modelled 98.6 28 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Short-chain ferredoxins
108d1rgva_



not modelled 98.6 26 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Short-chain ferredoxins
109c2yicC_



not modelled 98.6 17 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)
110c2fgoA_



not modelled 98.6 28 PDB header:electron transport
Chain: A: PDB Molecule:ferredoxin;
PDBTitle: structure of the 2[4fe-4s] ferredoxin from pseudomonas2 aeruginosa
111d2gmha3



not modelled 98.6 14 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:ETF-QO domain-like
112d1clfa_



not modelled 98.5 25 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Short-chain ferredoxins
113d1w85b2



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
114c2v2kB_



not modelled 98.5 27 PDB header:electron transport
Chain: B: PDB Molecule:ferredoxin;
PDBTitle: the crystal structure of fdxa, a 7fe ferredoxin from2 mycobacterium smegmatis
115d1ovma2



not modelled 98.5 13 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
116c1ti2F_



not modelled 98.5 21 PDB header:oxidoreductase
Chain: F: PDB Molecule:pyrogallol hydroxytransferase small subunit;
PDBTitle: crystal structure of pyrogallol-phloroglucinol2 transhydroxylase from pelobacter acidigallici
117d1kqfb1



not modelled 98.5 27 Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
118c1c4cA_



not modelled 98.5 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:protein (fe-only hydrogenase);
PDBTitle: binding of exogenously added carbon monoxide at the active2 site of the fe-only hydrogenase (cpi) from clostridium3 pasteurianum
119c2ivfB_



not modelled 98.5 37 PDB header:oxidoreductase
Chain: B: PDB Molecule:ethylbenzene dehydrogenase beta-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum
120d1zpda3



not modelled 98.5 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module

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