Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3EXH

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005730	cellular_component	nucleolus
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0006006	biological_process	glucose metabolic process
A	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
A	0006099	biological_process	tricarboxylic acid cycle
A	0016491	molecular_function	oxidoreductase activity
A	0016624	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
A	0043231	cellular_component	intracellular membrane-bounded organelle
A	0045254	cellular_component	pyruvate dehydrogenase complex
A	0046872	molecular_function	metal ion binding
A	1990204	cellular_component	oxidoreductase complex
B	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0006006	biological_process	glucose metabolic process
B	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
B	0006099	biological_process	tricarboxylic acid cycle
B	0016491	molecular_function	oxidoreductase activity
B	0044272	biological_process	sulfur compound biosynthetic process
B	0045254	cellular_component	pyruvate dehydrogenase complex
B	0046872	molecular_function	metal ion binding
B	0072522	biological_process	purine-containing compound biosynthetic process
C	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005730	cellular_component	nucleolus
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0006006	biological_process	glucose metabolic process
C	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
C	0006099	biological_process	tricarboxylic acid cycle
C	0016491	molecular_function	oxidoreductase activity
C	0016624	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
C	0043231	cellular_component	intracellular membrane-bounded organelle
C	0045254	cellular_component	pyruvate dehydrogenase complex
C	0046872	molecular_function	metal ion binding
C	1990204	cellular_component	oxidoreductase complex
D	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0006006	biological_process	glucose metabolic process
D	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
D	0006099	biological_process	tricarboxylic acid cycle
D	0016491	molecular_function	oxidoreductase activity
D	0044272	biological_process	sulfur compound biosynthetic process
D	0045254	cellular_component	pyruvate dehydrogenase complex
D	0046872	molecular_function	metal ion binding
D	0072522	biological_process	purine-containing compound biosynthetic process
E	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005730	cellular_component	nucleolus
E	0005739	cellular_component	mitochondrion
E	0005759	cellular_component	mitochondrial matrix
E	0006006	biological_process	glucose metabolic process
E	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
E	0006099	biological_process	tricarboxylic acid cycle
E	0016491	molecular_function	oxidoreductase activity
E	0016624	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
E	0043231	cellular_component	intracellular membrane-bounded organelle
E	0045254	cellular_component	pyruvate dehydrogenase complex
E	0046872	molecular_function	metal ion binding
E	1990204	cellular_component	oxidoreductase complex
F	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005739	cellular_component	mitochondrion
F	0005759	cellular_component	mitochondrial matrix
F	0006006	biological_process	glucose metabolic process
F	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
F	0006099	biological_process	tricarboxylic acid cycle
F	0016491	molecular_function	oxidoreductase activity
F	0044272	biological_process	sulfur compound biosynthetic process
F	0045254	cellular_component	pyruvate dehydrogenase complex
F	0046872	molecular_function	metal ion binding
F	0072522	biological_process	purine-containing compound biosynthetic process
G	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005730	cellular_component	nucleolus
G	0005739	cellular_component	mitochondrion
G	0005759	cellular_component	mitochondrial matrix
G	0006006	biological_process	glucose metabolic process
G	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
G	0006099	biological_process	tricarboxylic acid cycle
G	0016491	molecular_function	oxidoreductase activity
G	0016624	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
G	0043231	cellular_component	intracellular membrane-bounded organelle
G	0045254	cellular_component	pyruvate dehydrogenase complex
G	0046872	molecular_function	metal ion binding
G	1990204	cellular_component	oxidoreductase complex
H	0004739	molecular_function	pyruvate dehydrogenase (acetyl-transferring) activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005739	cellular_component	mitochondrion
H	0005759	cellular_component	mitochondrial matrix
H	0006006	biological_process	glucose metabolic process
H	0006086	biological_process	pyruvate decarboxylation to acetyl-CoA
H	0006099	biological_process	tricarboxylic acid cycle
H	0016491	molecular_function	oxidoreductase activity
H	0044272	biological_process	sulfur compound biosynthetic process
H	0045254	cellular_component	pyruvate dehydrogenase complex
H	0046872	molecular_function	metal ion binding
H	0072522	biological_process	purine-containing compound biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN A1500

Chain	Residue
A	ASP167
A	ASN196
A	TYR198
A	TPP1502
A	HOH2220

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K A1501

Chain	Residue
D	HOH2467
D	ALA160
D	ILE161
D	ASP163
D	HOH2046

site_id	AC3
Number of Residues	23
Details	BINDING SITE FOR RESIDUE TPP A1502

Chain	Residue
A	TYR89
A	ARG90
A	GLY136
A	VAL138
A	GLY166
A	ASP167
A	GLY168
A	ALA169
A	ASN196
A	TYR198
A	GLY199
A	ARG259
A	MN1500
A	HOH2134
A	HOH2179
A	HOH2220
A	HOH2278
D	GLU28
D	ILE57
D	GLU59
D	MET81
D	PHE85
D	GLN88

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN C1500

Chain	Residue
C	ASP167
C	ASN196
C	TYR198
C	TPP1502
C	HOH2193

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K C1501

Chain	Residue
B	ARG75
B	ALA160
B	ILE161
B	ASP163
B	HOH2112
B	HOH2118

site_id	AC6
Number of Residues	26
Details	BINDING SITE FOR RESIDUE TPP C1502

Chain	Residue
B	GLU28
B	ILE57
B	GLU59
B	MET81
B	PHE85
B	GLN88
C	TYR89
C	ARG90
C	GLY136
C	ILE137
C	VAL138
C	GLY166
C	ASP167
C	GLY168
C	ALA169
C	ASN196
C	TYR198
C	GLY199
C	MET200
C	HIS263
C	MN1500
C	HOH2080
C	HOH2193
C	HOH2282
C	HOH2296
C	HOH2592

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN E1500

Chain	Residue
E	ASP167
E	ASN196
E	TPP1502
E	HOH2195
E	HOH2247

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE K E1501

Chain	Residue
H	ALA160
H	ILE161
H	ASP163
H	HOH2117

site_id	AC9
Number of Residues	22
Details	BINDING SITE FOR RESIDUE TPP E1502

Chain	Residue
H	PHE85
H	GLN88
E	TYR89
E	ARG90
E	GLY136
E	ILE137
E	VAL138
E	GLY166
E	ASP167
E	GLY168
E	ALA169
E	ASN196
E	MN1500
E	HOH2194
E	HOH2195
E	HOH2247
E	HOH2556
E	HOH2668
H	GLU28
H	ILE57
H	GLU59
H	MET81

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN G1500

Chain	Residue
G	ASP167
G	ASN196
G	TYR198
G	TPP1502
G	HOH2248

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K G1501

Chain	Residue
F	ARG75
F	ALA160
F	ILE161
F	ASP163
F	HOH2026
F	HOH2432

site_id	BC3
Number of Residues	24
Details	BINDING SITE FOR RESIDUE TPP G1502

Chain	Residue
F	GLU28
F	ILE57
F	GLU59
F	MET81
F	PHE85
F	GLN88
G	TYR89
G	ARG90
G	GLY136
G	VAL138
G	GLY166
G	ASP167
G	GLY168
G	ALA169
G	ASN196
G	TYR198
G	GLY199
G	MET200
G	HIS263
G	MN1500
G	HOH2015
G	HOH2052
G	HOH2248
G	HOH2474

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A1901

Chain	Residue
A	HOH2671
C	ASN130
C	TYR132
D	GLN108

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A1902

Chain	Residue
A	HOH2317
C	LYS153
C	TRP185
D	ASP49

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C1903

Chain	Residue
A	LYS153
A	TRP185
B	ASP49

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E1904

Chain	Residue
E	HOH2615
E	HOH2737
G	ASN130
G	TYR132
H	MET71
H	GLN108

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL G1905

Chain	Residue
A	ASP343
B	LYS143
B	ILE195
G	HOH2684
G	HOH2709

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	11
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29970614","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"6CFO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NI4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	12
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	8
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	3
Details	Modified 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine; by PDK1, PDK2, PDK3 and PDK4","evidences":[{"source":"PubMed","id":"11486000","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19081061","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	3
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P35486","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12651851","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	4
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	8
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	4
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	4
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	4
Details	Site: {"description":"Important for interaction with DLAT","evidences":[{"source":"PubMed","id":"20160912","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q9D051","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9D051","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified 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"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
A	HIS263

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
F	GLU59
F	HIS128

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
H	GLU59
H	HIS128

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
C	HIS263

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
G	HIS263

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
B	GLU59

site_id	CSA5
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
D	GLU59

site_id	CSA6
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
F	GLU59

site_id	CSA7
Number of Residues	1
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
H	GLU59

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
B	GLU59
B	HIS128

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1dtw

Chain	Residue	Details
D	GLU59
D	HIS128

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)