Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3VAZ

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group

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	0005737	cellular_component	cytoplasm
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	0030554	molecular_function	adenyl nucleotide binding
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
B	0000166	molecular_function	nucleotide binding
B	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B	0005737	cellular_component	cytoplasm
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	0030554	molecular_function	adenyl nucleotide binding
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
O	0000166	molecular_function	nucleotide binding
O	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
O	0005737	cellular_component	cytoplasm
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	0030554	molecular_function	adenyl nucleotide binding
O	0050661	molecular_function	NADP binding
O	0051287	molecular_function	NAD binding
P	0000166	molecular_function	nucleotide binding
P	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
P	0005737	cellular_component	cytoplasm
P	0006006	biological_process	glucose metabolic process
P	0006096	biological_process	glycolytic process
P	0016491	molecular_function	oxidoreductase activity
P	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
P	0030554	molecular_function	adenyl nucleotide binding
P	0050661	molecular_function	NADP binding
P	0051287	molecular_function	NAD binding
Q	0000166	molecular_function	nucleotide binding
Q	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
Q	0005737	cellular_component	cytoplasm
Q	0006006	biological_process	glucose metabolic process
Q	0006096	biological_process	glycolytic process
Q	0016491	molecular_function	oxidoreductase activity
Q	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Q	0030554	molecular_function	adenyl nucleotide binding
Q	0050661	molecular_function	NADP binding
Q	0051287	molecular_function	NAD binding
R	0000166	molecular_function	nucleotide binding
R	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
R	0005737	cellular_component	cytoplasm
R	0006006	biological_process	glucose metabolic process
R	0006096	biological_process	glycolytic process
R	0016491	molecular_function	oxidoreductase activity
R	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
R	0030554	molecular_function	adenyl nucleotide binding
R	0050661	molecular_function	NADP binding
R	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAD P 401

Chain	Residue
P	GLY9
P	THR97
P	GLY98
P	SER120
P	ALA121
P	ASN316
P	TYR320
P	HOH501
P	HOH505
Q	PRO190
P	GLY11
P	ARG12
P	ILE13
P	ASN33
P	ASP34
P	LEU35
P	PRO78
P	CYS96

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 P 402

Chain	Residue
B	ASP37
B	ASP39
P	ASP38
P	GLY63
P	SER74

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 P 403

Chain	Residue
B	ASP38
B	GLY63
B	SER74
P	ASP37
P	ASP39

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 P 404

Chain	Residue
A	ARG192
A	LYS193
A	GLY194
P	SER76
P	HOH523

site_id	AC5
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAD R 401

Chain	Residue
O	PRO190
O	HOH545
R	GLY9
R	GLY11
R	ARG12
R	ILE13
R	ASP34
R	LEU35
R	PRO78
R	CYS96
R	THR97
R	GLY98
R	SER120
R	ALA121
R	CYS151
R	ASN316
R	TYR320
R	HOH555

site_id	AC6
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NAD O 401

Chain	Residue
O	GLY9
O	PHE10
O	GLY11
O	ARG12
O	ILE13
O	ASN33
O	ASP34
O	LEU35
O	PRO78
O	CYS96
O	THR97
O	GLY98
O	PHE99
O	SER120
O	ALA121
O	ASN316
O	TYR320
O	HOH513
R	PRO190

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 O 402

Chain	Residue
O	SER76
O	LYS82

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DGY O 403

Chain	Residue
A	HOH522
O	ASP166
O	HOH506
O	HOH507

site_id	AC9
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD Q 401

Chain	Residue
P	PRO190
P	HOH573
Q	GLY9
Q	GLY11
Q	ARG12
Q	ILE13
Q	ASN33
Q	ASP34
Q	LEU35
Q	PRO78
Q	CYS96
Q	THR97
Q	GLY98
Q	PHE99
Q	SER120
Q	ALA121
Q	CYS151
Q	ASN316
Q	TYR320
Q	HOH516
Q	HOH520
Q	HOH547

site_id	BC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAD B 401

Chain	Residue
A	HOH555
B	GLY9
B	GLY11
B	ARG12
B	ILE13
B	ASN33
B	ASP34
B	LEU35
B	PRO78
B	CYS96
B	THR97
B	GLY98
B	SER120
B	ALA121
B	ASN316
B	TYR320
B	HOH501
B	HOH503
B	HOH518
B	HOH534
B	HOH538
B	HOH540
A	PRO190

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 B 402

Chain	Residue
B	SER76
B	HOH560
Q	ARG192
Q	LYS193
Q	GLY194

site_id	BC3
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD A 401

Chain	Residue
A	GLY9
A	GLY11
A	ARG12
A	ILE13
A	ASN33
A	ASP34
A	LEU35
A	PRO78
A	CYS96
A	THR97
A	GLY98
A	PHE99
A	SER120
A	ALA121
A	ASN316
A	TYR320
A	HOH503
A	HOH518
A	HOH525
A	HOH541

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 A 402

Chain	Residue
A	LYS4
A	ASN89
A	ASP91
A	LYS115
O	GLU138

site_id	BC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE DGY A 403

Chain	Residue
A	ASP165
A	ASP165
A	ASP166
A	ASP166
A	PHE167
A	PHE167
A	HOH526
A	HOH546
A	HOH570
A	HOH570

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
P	ALA149-LEU156

site_id	PS00211
Number of Residues	15
Details	ABC_TRANSPORTER_1 ABC transporters family signature. MSVGDRQLVKVAAWY

Chain	Residue	Details
P	MET300-TYR314

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Nucleophile => ECO:0000269\|PubMed:20620151

Chain	Residue	Details
P	CYS151
R	CYS151
O	CYS151
Q	CYS151
B	CYS151
A	CYS151

site_id	SWS_FT_FI2
Number of Residues	18
Details	BINDING: BINDING => ECO:0000269\|PubMed:20620151, ECO:0000269\|Ref.3

Chain	Residue	Details
P	ARG12
Q	ARG12
Q	ASP34
Q	SER120
B	ARG12
B	ASP34
B	SER120
A	ARG12
A	ASP34
A	SER120
P	ASP34
P	SER120
R	ARG12
R	ASP34
R	SER120
O	ARG12
O	ASP34
O	SER120

site_id	SWS_FT_FI3
Number of Residues	30
Details	BINDING: BINDING => ECO:0000269\|PubMed:20620151

Chain	Residue	Details
P	SER150
R	ASN316
O	SER150
O	THR181
O	THR211
O	ARG234
O	ASN316
Q	SER150
Q	THR181
Q	THR211
Q	ARG234
P	THR181
Q	ASN316
B	SER150
B	THR181
B	THR211
B	ARG234
B	ASN316
A	SER150
A	THR181
A	THR211
A	ARG234
P	THR211
A	ASN316
P	ARG234
P	ASN316
R	SER150
R	THR181
R	THR211
R	ARG234

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P00362

Chain	Residue	Details
P	ARG198
R	ARG198
O	ARG198
Q	ARG198
B	ARG198
A	ARG198

site_id	SWS_FT_FI5
Number of Residues	6
Details	SITE: Activates thiol group during catalysis => ECO:0000269\|PubMed:20620151

Chain	Residue	Details
P	HIS178
R	HIS178
O	HIS178
Q	HIS178
B	HIS178
A	HIS178

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