Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2VYN

Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006006	biological_process	glucose metabolic process
A	0006096	biological_process	glycolytic process
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
A	0042802	molecular_function	identical protein binding
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
A	0072524	biological_process	pyridine-containing compound metabolic process
B	0000166	molecular_function	nucleotide binding
B	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006006	biological_process	glucose metabolic process
B	0006096	biological_process	glycolytic process
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
B	0042802	molecular_function	identical protein binding
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
B	0072524	biological_process	pyridine-containing compound metabolic process
C	0000166	molecular_function	nucleotide binding
C	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006006	biological_process	glucose metabolic process
C	0006096	biological_process	glycolytic process
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
C	0042802	molecular_function	identical protein binding
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
C	0072524	biological_process	pyridine-containing compound metabolic process
D	0006006	biological_process	glucose metabolic process
D	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
D	0050661	molecular_function	NADP binding
D	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FMT A1332

Chain	Residue
A	PRO126
A	MET127
A	ASN133
A	LYS215
A	HOH2205

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FMT C1332

Chain	Residue
C	PRO126
C	MET127
C	LYS215
C	HOH2180

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE FMT D1336

Chain	Residue
D	MET126
D	HOH2209
D	HOH2210

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FMT B1332

Chain	Residue
B	PRO126
B	MET127
B	LYS215
B	HOH2201
B	HOH2202

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE FMT D1337

Chain	Residue
C	GLU285
D	ARG51

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE FMT B1333

Chain	Residue
A	ARG51
B	ASP281
B	GLU285

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FMT D1338

Chain	Residue
D	PRO120
D	SER148
D	THR151
D	GLY209
D	ALA210
D	ALA213
D	HOH2211
D	HOH2212
D	HOH2214

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE FMT D1339

Chain	Residue
D	GLY130
D	GLU133

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE FMT A1333

Chain	Residue
A	ARG51
B	THR273

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE FMT B1334

Chain	Residue
B	THR273
B	GLU274
B	ASP275

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FMT A1334

Chain	Residue
A	GLY131
A	ALA132
A	PHE134
A	ASP135
A	HOH2206
A	HOH2207

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FMT B1335

Chain	Residue
B	GLY131
B	ALA132
B	ASN133
B	PHE134
B	ASP135

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FMT D1340

Chain	Residue
D	ARG17
D	GLU21
D	HIS49
D	HOH2215

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FMT C1333

Chain	Residue
C	GLY131
C	ALA132
C	ASN133
C	PHE134

site_id	BC6
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD A1335

Chain	Residue
A	ASN6
A	GLY7
A	PHE8
A	GLY9
A	ARG10
A	ILE11
A	ASN31
A	ASP32
A	LEU33
A	GLU75
A	ARG76
A	ALA94
A	THR95
A	GLY96
A	LEU97
A	THR118
A	CSD148
A	ALA179
A	ASN312
A	TYR316
A	HOH2002
A	HOH2066
A	HOH2103
A	HOH2192
A	HOH2208
A	HOH2209
A	HOH2210
A	HOH2211
A	HOH2213
A	HOH2214
A	HOH2215
A	HOH2216
D	PRO188

site_id	BC7
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD B1336

Chain	Residue
B	GLU75
B	ARG76
B	ALA94
B	THR95
B	GLY96
B	LEU97
B	THR118
B	CSD148
B	ALA179
B	ASN312
B	TYR316
B	HOH2002
B	HOH2095
B	HOH2186
B	HOH2203
B	HOH2204
B	HOH2206
B	HOH2207
B	HOH2208
B	HOH2209
B	HOH2210
B	HOH2211
C	PRO187
B	ASN6
B	GLY7
B	PHE8
B	GLY9
B	ARG10
B	ILE11
B	ASN31
B	ASP32
B	LEU33

site_id	BC8
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD C1334

Chain	Residue
B	PRO187
C	ASN6
C	GLY7
C	PHE8
C	GLY9
C	ARG10
C	ILE11
C	ASN31
C	ASP32
C	LEU33
C	ARG76
C	ALA94
C	THR95
C	GLY96
C	LEU97
C	PHE98
C	THR118
C	CSD148
C	ALA179
C	ASN312
C	TYR316
C	HOH2002
C	HOH2167
C	HOH2177
C	HOH2182
C	HOH2183
C	HOH2184
C	HOH2185
C	HOH2186
C	HOH2187
C	HOH2188
C	HOH2189

site_id	BC9
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAD D1341

Chain	Residue
D	ASN6
D	GLY7
D	PHE8
D	GLY9
D	ARG10
D	ILE11
D	ASN30
D	ASP31
D	PRO32
D	PHE33
D	CSX75
D	LYS76
D	ALA94
D	THR95
D	GLY96
D	THR118
D	ALA119
D	CSD149
D	ALA180
D	ASN313
D	TYR317
D	HOH2107
D	HOH2199
D	HOH2216
D	HOH2217
D	HOH2218
D	HOH2219
D	HOH2220
D	HOH2221
D	HOH2222
D	HOH2223
D	HOH2224
D	HOH2225
D	HOH2226

Functional Information from PROSITE/UniProt

site_id	PS00071
Number of Residues	8
Details	GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNcL

Chain	Residue	Details
D	ALA147-LEU154
A	ALA146-LEU153

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"10978154","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10978154","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19542219","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8636984","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2004","submissionDatabase":"PDB data bank","title":"Crystal structure of MES buffer bound form of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli.","authors":["Shin D.H.","Thor J.","Yokota H.","Kim R.","Kim S.H."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10978154","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19542219","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8636984","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10978154","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19542219","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19542219","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P00362","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10978154","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19542219","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2004","submissionDatabase":"PDB data bank","title":"Crystal structure of MES buffer bound form of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli.","authors":["Shin D.H.","Thor J.","Yokota H.","Kim R.","Kim S.H."]}},{"source":"PubMed","id":"10978154","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	3
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"PubMed","id":"2659073","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	24
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"21151122","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"21151122","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU10009","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	9
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	1
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"22673903","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

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

Chain	Residue	Details
D	HIS176

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

Chain	Residue	Details
A	HIS175

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

Chain	Residue	Details
B	HIS175

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

Chain	Residue	Details
C	HIS175

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