Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3E5R

Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006006	biological_process	glucose metabolic process
A	0006096	biological_process	glycolytic process
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	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
B	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006006	biological_process	glucose metabolic process
B	0006096	biological_process	glycolytic process
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	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
C	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006006	biological_process	glucose metabolic process
C	0006096	biological_process	glycolytic process
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	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
O	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
O	0005737	cellular_component	cytoplasm
O	0005829	cellular_component	cytosol
O	0006006	biological_process	glucose metabolic process
O	0006096	biological_process	glycolytic process
O	0016491	molecular_function	oxidoreductase activity
O	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
O	0050661	molecular_function	NADP binding
O	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD O 5463

Chain	Residue
B	PRO193
O	PRO36
O	THR101
O	GLY102
O	SER124
O	ALA125
O	CYS154
O	ALA185
O	ASN318
O	GLU319
O	HOH5493
O	ASN9
O	HOH5521
O	HOH5559
O	GLY10
O	PHE11
O	GLY12
O	ARG13
O	ILE14
O	ASN34
O	ASP35

site_id	AC2
Number of Residues	25
Details	BINDING SITE FOR RESIDUE NAD A 5466

Chain	Residue
A	ASN9
A	GLY10
A	PHE11
A	GLY12
A	ARG13
A	ILE14
A	ASN34
A	ASP35
A	PRO36
A	PHE37
A	ARG82
A	THR101
A	GLY102
A	PHE104
A	SER124
A	ALA125
A	PRO126
A	CYS154
A	ALA185
A	ASN318
A	TYR322
A	HOH5626
A	HOH5684
C	PRO193
C	HOH5801

site_id	AC3
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAD B 5465

Chain	Residue
B	ASN9
B	GLY10
B	PHE11
B	GLY12
B	ARG13
B	ILE14
B	ASN34
B	ASP35
B	PRO36
B	PHE37
B	ILE38
B	ARG82
B	THR101
B	GLY102
B	PHE104
B	SER124
B	ALA125
B	CYS154
B	ALA185
B	ASN318
B	GLU319
B	TYR322
B	HOH5485
B	HOH5527
B	HOH5562
B	HOH5573
B	HOH5657
O	HOH5551

site_id	AC4
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAD C 5467

Chain	Residue
C	HOH5797
A	PRO193
A	HOH5768
C	ASN9
C	GLY10
C	PHE11
C	GLY12
C	ARG13
C	ILE14
C	ASN34
C	ASP35
C	PRO36
C	PHE37
C	ILE38
C	ARG82
C	THR101
C	GLY102
C	SER124
C	ALA125
C	CYS154
C	ALA185
C	ASN318
C	GLU319
C	TYR322
C	HOH5607
C	HOH5614

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
O	ALA152-LEU159

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Nucleophile => ECO:0000255\|PROSITE-ProRule:PRU10009

Chain	Residue	Details
O	CYS154
A	CYS154
B	CYS154
C	CYS154

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:22903596

Chain	Residue	Details
O	ARG13
C	ARG13
C	ASP35
C	ARG82
O	ASP35
O	ARG82
A	ARG13
A	ASP35
A	ARG82
B	ARG13
B	ASP35
B	ARG82

site_id	SWS_FT_FI3
Number of Residues	20
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
O	SER153
A	ASN318
B	SER153
B	THR184
B	THR213
B	ARG236
B	ASN318
C	SER153
C	THR184
C	THR213
C	ARG236
O	THR184
C	ASN318
O	THR213
O	ARG236
O	ASN318
A	SER153
A	THR184
A	THR213
A	ARG236

site_id	SWS_FT_FI4
Number of Residues	4
Details	SITE: Activates thiol group during catalysis => ECO:0000250

Chain	Residue	Details
O	HIS181
A	HIS181
B	HIS181
C	HIS181

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
O	HIS181
O	CYS154

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
A	HIS181
A	CYS154

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
B	HIS181
B	CYS154

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
C	HIS181
C	CYS154

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