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3EXE

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005739cellular_componentmitochondrion
A0005759cellular_componentmitochondrial matrix
A0006006biological_processglucose metabolic process
A0006086biological_processpyruvate decarboxylation to acetyl-CoA
A0006099biological_processtricarboxylic acid cycle
A0016491molecular_functionoxidoreductase activity
A0016624molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
A0032991cellular_componentprotein-containing complex
A0043231cellular_componentintracellular membrane-bounded organelle
A0045254cellular_componentpyruvate dehydrogenase complex
A0046872molecular_functionmetal ion binding
B0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005739cellular_componentmitochondrion
B0005759cellular_componentmitochondrial matrix
B0006006biological_processglucose metabolic process
B0006086biological_processpyruvate decarboxylation to acetyl-CoA
B0006099biological_processtricarboxylic acid cycle
B0009060biological_processaerobic respiration
B0016491molecular_functionoxidoreductase activity
B0044272biological_processsulfur compound biosynthetic process
B0045254cellular_componentpyruvate dehydrogenase complex
B0046872molecular_functionmetal ion binding
B0072522biological_processpurine-containing compound biosynthetic process
C0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005739cellular_componentmitochondrion
C0005759cellular_componentmitochondrial matrix
C0006006biological_processglucose metabolic process
C0006086biological_processpyruvate decarboxylation to acetyl-CoA
C0006099biological_processtricarboxylic acid cycle
C0016491molecular_functionoxidoreductase activity
C0016624molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
C0032991cellular_componentprotein-containing complex
C0043231cellular_componentintracellular membrane-bounded organelle
C0045254cellular_componentpyruvate dehydrogenase complex
C0046872molecular_functionmetal ion binding
D0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005739cellular_componentmitochondrion
D0005759cellular_componentmitochondrial matrix
D0006006biological_processglucose metabolic process
D0006086biological_processpyruvate decarboxylation to acetyl-CoA
D0006099biological_processtricarboxylic acid cycle
D0009060biological_processaerobic respiration
D0016491molecular_functionoxidoreductase activity
D0044272biological_processsulfur compound biosynthetic process
D0045254cellular_componentpyruvate dehydrogenase complex
D0046872molecular_functionmetal ion binding
D0072522biological_processpurine-containing compound biosynthetic process
E0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005739cellular_componentmitochondrion
E0005759cellular_componentmitochondrial matrix
E0006006biological_processglucose metabolic process
E0006086biological_processpyruvate decarboxylation to acetyl-CoA
E0006099biological_processtricarboxylic acid cycle
E0016491molecular_functionoxidoreductase activity
E0016624molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
E0032991cellular_componentprotein-containing complex
E0043231cellular_componentintracellular membrane-bounded organelle
E0045254cellular_componentpyruvate dehydrogenase complex
E0046872molecular_functionmetal ion binding
F0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005739cellular_componentmitochondrion
F0005759cellular_componentmitochondrial matrix
F0006006biological_processglucose metabolic process
F0006086biological_processpyruvate decarboxylation to acetyl-CoA
F0006099biological_processtricarboxylic acid cycle
F0009060biological_processaerobic respiration
F0016491molecular_functionoxidoreductase activity
F0044272biological_processsulfur compound biosynthetic process
F0045254cellular_componentpyruvate dehydrogenase complex
F0046872molecular_functionmetal ion binding
F0072522biological_processpurine-containing compound biosynthetic process
G0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005739cellular_componentmitochondrion
G0005759cellular_componentmitochondrial matrix
G0006006biological_processglucose metabolic process
G0006086biological_processpyruvate decarboxylation to acetyl-CoA
G0006099biological_processtricarboxylic acid cycle
G0016491molecular_functionoxidoreductase activity
G0016624molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
G0032991cellular_componentprotein-containing complex
G0043231cellular_componentintracellular membrane-bounded organelle
G0045254cellular_componentpyruvate dehydrogenase complex
G0046872molecular_functionmetal ion binding
H0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005739cellular_componentmitochondrion
H0005759cellular_componentmitochondrial matrix
H0006006biological_processglucose metabolic process
H0006086biological_processpyruvate decarboxylation to acetyl-CoA
H0006099biological_processtricarboxylic acid cycle
H0009060biological_processaerobic respiration
H0016491molecular_functionoxidoreductase activity
H0044272biological_processsulfur compound biosynthetic process
H0045254cellular_componentpyruvate dehydrogenase complex
H0046872molecular_functionmetal ion binding
H0072522biological_processpurine-containing compound biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN C 1001
ChainResidue
CASP167
CASN196
CTYR198
CTPP1002
CHOH2234

site_idAC2
Number of Residues24
DetailsBINDING SITE FOR RESIDUE TPP C 1002
ChainResidue
BGLN88
CTYR89
CARG90
CGLY136
CVAL138
CGLY166
CASP167
CGLY168
CALA169
CASN196
CTYR198
CGLY199
CMET200
CHIS263
CMN1001
CHOH2200
CHOH2222
CHOH2234
CHOH2277
CHOH2489
BGLU28
BILE57
BGLU59
BPHE85

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K B 1003
ChainResidue
BALA160
BILE161
BASP163
BHOH2133
BHOH2301

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN A 1004
ChainResidue
AASP167
AASN196
ATYR198
ATPP1005
AHOH2039

site_idAC5
Number of Residues23
DetailsBINDING SITE FOR RESIDUE TPP A 1005
ChainResidue
ATYR89
AARG90
AGLY136
AVAL138
AGLY166
AASP167
AGLY168
AALA169
AASN196
ATYR198
AGLY199
AHIS263
AMN1004
AHOH2039
AHOH2043
AHOH2122
AHOH2149
AHOH2346
DGLU28
DILE57
DGLU59
DPHE85
DGLN88

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE K D 1006
ChainResidue
DARG75
DALA160
DILE161
DASP163
DHOH2065
DHOH2159

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN G 1007
ChainResidue
GASP167
GASN196
GTYR198
GTPP1008
GHOH2294

site_idAC8
Number of Residues25
DetailsBINDING SITE FOR RESIDUE TPP G 1008
ChainResidue
FGLU28
FILE57
FGLU59
FMET81
FPHE85
FGLN88
GTYR89
GARG90
GGLY136
GVAL138
GGLY166
GASP167
GGLY168
GALA169
GASN196
GTYR198
GGLY199
GMET200
GHIS263
GMN1007
GHOH2062
GHOH2249
GHOH2294
GHOH2355
GHOH2447

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE K F 1009
ChainResidue
FALA160
FILE161
FASP163
FHOH2116
FHOH2636
FARG75

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN E 1010
ChainResidue
EASP167
EASN196
ETYR198
ETPP1011
EHOH2223

site_idBC2
Number of Residues24
DetailsBINDING SITE FOR RESIDUE TPP E 1011
ChainResidue
ETYR89
EARG90
EGLY136
EVAL138
EGLY166
EASP167
EGLY168
EALA169
EASN196
ETYR198
EGLY199
EMET200
EHIS263
EMN1010
EHOH2130
EHOH2179
EHOH2223
EHOH2391
EHOH2500
HGLU28
HILE57
HGLU59
HPHE85
HGLN88

site_idBC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K H 1012
ChainResidue
HALA160
HILE161
HASP163
HHOH2386
HHOH2397

site_idBC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL A 1101
ChainResidue
ALYS153
ATRP185
ALEU187
AHOH2650
AHOH2946
AHOH3205
BASP49
BILE53

site_idBC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL C 1102
ChainResidue
CLYS153
CTRP185
CHOH2477
CHOH2998
CHOH3876
DASP49
DILE53
DHOH2905

site_idBC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL E 1103
ChainResidue
ELYS153
ELEU187
EHOH2656
EHOH3689
EHOH3731
FASP49
FILE53

site_idBC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL G 1104
ChainResidue
GLYS153
GLEU187
GHOH3129
GHOH3379
HASP49
HILE53
HHOH2848

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"29970614","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"6CFO","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues16
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29970614","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CER","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXH","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues12
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine; by PDK1","evidences":[{"source":"PubMed","id":"11486000","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues8
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine; by PDK1, PDK2, PDK3 and PDK4","evidences":[{"source":"PubMed","id":"11486000","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine; by PDK1, PDK2, PDK3 and PDK4","evidences":[{"source":"PubMed","id":"11486000","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues4
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues4
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI16
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZL","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI17
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI18
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3EXE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI19
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17474719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EXE","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI20
Number of Residues4
DetailsSite: {"description":"Important for interaction with DLAT","evidences":[{"source":"PubMed","id":"20160912","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI21
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q9D051","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI22
Number of Residues4
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9D051","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
AHIS263

site_idCSA10
Number of Residues2
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
DGLU59
DHIS128

site_idCSA11
Number of Residues2
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
FGLU59
FHIS128

site_idCSA12
Number of Residues2
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
HGLU59
HHIS128

site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
CHIS263

site_idCSA3
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
EHIS263

site_idCSA4
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
GHIS263

site_idCSA5
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
BGLU59

site_idCSA6
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
DGLU59

site_idCSA7
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
FGLU59

site_idCSA8
Number of Residues1
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
HGLU59

site_idCSA9
Number of Residues2
DetailsAnnotated By Reference To The Literature 1dtw
ChainResidueDetails
BGLU59
BHIS128

247536

PDB entries from 2026-01-14

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