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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3EXF

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
A0005730cellular_componentnucleolus
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
A0043231cellular_componentintracellular membrane-bounded organelle
A0045254cellular_componentpyruvate dehydrogenase complex
A0046872molecular_functionmetal ion binding
A1990204cellular_componentoxidoreductase complex
B0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005739cellular_componentmitochondrion
B0005759cellular_componentmitochondrial matrix
B0006006biological_processglucose metabolic process
B0006086biological_processpyruvate decarboxylation to acetyl-CoA
B0006099biological_processtricarboxylic acid cycle
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
C0005730cellular_componentnucleolus
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
C0043231cellular_componentintracellular membrane-bounded organelle
C0045254cellular_componentpyruvate dehydrogenase complex
C0046872molecular_functionmetal ion binding
C1990204cellular_componentoxidoreductase complex
D0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005739cellular_componentmitochondrion
D0005759cellular_componentmitochondrial matrix
D0006006biological_processglucose metabolic process
D0006086biological_processpyruvate decarboxylation to acetyl-CoA
D0006099biological_processtricarboxylic acid cycle
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
E0005730cellular_componentnucleolus
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
E0043231cellular_componentintracellular membrane-bounded organelle
E0045254cellular_componentpyruvate dehydrogenase complex
E0046872molecular_functionmetal ion binding
E1990204cellular_componentoxidoreductase complex
F0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005739cellular_componentmitochondrion
F0005759cellular_componentmitochondrial matrix
F0006006biological_processglucose metabolic process
F0006086biological_processpyruvate decarboxylation to acetyl-CoA
F0006099biological_processtricarboxylic acid cycle
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
G0005730cellular_componentnucleolus
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
G0043231cellular_componentintracellular membrane-bounded organelle
G0045254cellular_componentpyruvate dehydrogenase complex
G0046872molecular_functionmetal ion binding
G1990204cellular_componentoxidoreductase complex
H0004739molecular_functionpyruvate dehydrogenase (acetyl-transferring) activity
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
H0005739cellular_componentmitochondrion
H0005759cellular_componentmitochondrial matrix
H0006006biological_processglucose metabolic process
H0006086biological_processpyruvate decarboxylation to acetyl-CoA
H0006099biological_processtricarboxylic acid cycle
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 Residues4
DetailsBINDING SITE FOR RESIDUE MG A1001
ChainResidue
AASP167
AASN196
ATYR198
ATPP1003
site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K D1002
ChainResidue
DARG75
DPRO111
DALA160
DILE161
DASP163
site_idAC3
Number of Residues19
DetailsBINDING SITE FOR RESIDUE TPP A1003
ChainResidue
ATYR89
AARG90
AGLY136
AVAL138
AGLY166
AASP167
AGLY168
AALA169
AASN196
ATYR198
AGLY199
AMET200
AHIS263
AMG1001
DGLU28
DILE57
DGLU59
DPHE85
DGLN88
site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C1004
ChainResidue
CASP167
CASN196
CTYR198
CTPP1006
CHOH2002
site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B1005
ChainResidue
BILE112
BALA160
BILE161
BASP163
site_idAC6
Number of Residues20
DetailsBINDING SITE FOR RESIDUE TPP C1006
ChainResidue
BGLU28
BILE57
BGLU59
BPHE85
BGLN88
CTYR89
CARG90
CGLY136
CILE137
CVAL138
CGLY166
CASP167
CGLY168
CALA169
CASN196
CTYR198
CGLY199
CMET200
CMG1004
CHOH2002
site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG E1007
ChainResidue
EASP167
EASN196
ETYR198
ETPP1009
site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE K H1008
ChainResidue
HPRO111
HILE112
HVAL113
HALA160
HILE161
HASP163
site_idAC9
Number of Residues20
DetailsBINDING SITE FOR RESIDUE TPP E1009
ChainResidue
ETYR89
EARG90
EGLY136
EVAL138
EGLY166
EASP167
EGLY168
EALA169
EGLN172
EASN196
ETYR198
EGLY199
EMET200
EHIS263
EMG1007
HGLU28
HILE57
HGLU59
HPHE85
HGLN88
site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG G1010
ChainResidue
GASP167
GASN196
GTYR198
GTPP1012
site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K F1011
ChainResidue
FARG75
FPRO111
FALA160
FILE161
FASP163
site_idBC3
Number of Residues19
DetailsBINDING SITE FOR RESIDUE TPP G1012
ChainResidue
FPHE85
FGLN88
GTYR89
GARG90
GGLY136
GVAL138
GGLY166
GASP167
GGLY168
GALA169
GASN196
GTYR198
GGLY199
GMET200
GHIS263
GMG1010
FGLU28
FILE57
FGLU59
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

244693

PDB entries from 2025-11-12

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