Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VMT

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0005737	cellular_component	cytoplasm
A	0006006	biological_process	glucose metabolic 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	0000166	molecular_function	nucleotide binding
B	0005737	cellular_component	cytoplasm
B	0006006	biological_process	glucose metabolic 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	0000166	molecular_function	nucleotide binding
C	0005737	cellular_component	cytoplasm
C	0006006	biological_process	glucose metabolic 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
D	0000166	molecular_function	nucleotide binding
D	0005737	cellular_component	cytoplasm
D	0006006	biological_process	glucose metabolic process
D	0016491	molecular_function	oxidoreductase activity
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
E	0000166	molecular_function	nucleotide binding
E	0005737	cellular_component	cytoplasm
E	0006006	biological_process	glucose metabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
E	0050661	molecular_function	NADP binding
E	0051287	molecular_function	NAD binding
F	0000166	molecular_function	nucleotide binding
F	0005737	cellular_component	cytoplasm
F	0006006	biological_process	glucose metabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
F	0050661	molecular_function	NADP binding
F	0051287	molecular_function	NAD binding
G	0000166	molecular_function	nucleotide binding
G	0005737	cellular_component	cytoplasm
G	0006006	biological_process	glucose metabolic process
G	0016491	molecular_function	oxidoreductase activity
G	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
G	0050661	molecular_function	NADP binding
G	0051287	molecular_function	NAD binding
H	0000166	molecular_function	nucleotide binding
H	0005737	cellular_component	cytoplasm
H	0006006	biological_process	glucose metabolic process
H	0016491	molecular_function	oxidoreductase activity
H	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
H	0050661	molecular_function	NADP binding
H	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	27
Details	binding site for residue NAD A 401

Chain	Residue
A	GLY9
A	GLY98
A	PHE99
A	PHE100
A	SER120
A	ALA121
A	CYS151
A	ASN315
A	TYR319
A	HOH519
A	HOH529
A	GLY11
A	HOH534
A	HOH536
A	HOH541
A	HOH556
A	HOH573
A	HOH588
A	HOH603
C	PRO190
A	ARG12
A	ILE13
A	ASP34
A	LEU35
A	PRO78
A	CYS96
A	THR97

site_id	AC2
Number of Residues	2
Details	binding site for residue CL A 402

Chain	Residue
A	LYS308
B	GLY230

site_id	AC3
Number of Residues	2
Details	binding site for residue CL A 403

Chain	Residue
B	ARG297
B	LYS308

site_id	AC4
Number of Residues	29
Details	binding site for residue NAD B 401

Chain	Residue
B	GLY9
B	GLY11
B	ARG12
B	ILE13
B	ASP34
B	LEU35
B	PRO78
B	CYS96
B	THR97
B	GLY98
B	PHE99
B	PHE100
B	SER120
B	ALA121
B	CYS151
B	ASN315
B	TYR319
B	HOH509
B	HOH511
B	HOH538
B	HOH546
B	HOH550
B	HOH563
B	HOH565
B	HOH573
B	HOH574
B	HOH575
B	HOH603
D	PRO190

site_id	AC5
Number of Residues	14
Details	binding site for residue NAD C 401

Chain	Residue
A	PRO190
C	GLY9
C	GLY11
C	ARG12
C	ILE13
C	ASP34
C	CYS96
C	GLY98
C	PHE99
C	PHE100
C	SER120
C	ALA121
C	CYS151
C	ASN315

site_id	AC6
Number of Residues	3
Details	binding site for residue CL C 402

Chain	Residue
C	ARG297
C	LYS308
C	HOH546

site_id	AC7
Number of Residues	28
Details	binding site for residue NAD D 401

Chain	Residue
D	HOH548
D	HOH562
D	HOH577
D	HOH579
D	HOH598
D	HOH602
B	PRO190
D	GLY9
D	GLY11
D	ARG12
D	ILE13
D	ASN33
D	ASP34
D	LEU35
D	PRO78
D	CYS96
D	THR97
D	GLY98
D	PHE99
D	SER120
D	ALA121
D	CYS151
D	ASN315
D	TYR319
D	HOH506
D	HOH532
D	HOH539
D	HOH540

site_id	AC8
Number of Residues	2
Details	binding site for residue CL D 402

Chain	Residue
D	ARG297
D	LYS308

site_id	AC9
Number of Residues	16
Details	binding site for residue NAD E 401

Chain	Residue
E	GLY11
E	ARG12
E	ILE13
E	ASN33
E	ASP34
E	LEU35
E	CYS96
E	GLY98
E	PHE99
E	PHE100
E	SER120
E	ALA121
E	CYS151
E	ASN315
E	HOH532
G	PRO190

site_id	AD1
Number of Residues	4
Details	binding site for residue CL E 402

Chain	Residue
E	LYS308
E	HOH516
F	GLY230
F	SER231

site_id	AD2
Number of Residues	25
Details	binding site for residue NAD F 401

Chain	Residue
F	GLY9
F	GLY11
F	ARG12
F	ILE13
F	ASP34
F	LEU35
F	PRO78
F	CYS96
F	THR97
F	GLY98
F	PHE99
F	SER120
F	ALA121
F	CYS151
F	ASN315
F	TYR319
F	HOH512
F	HOH516
F	HOH553
F	HOH561
F	HOH563
F	HOH567
F	HOH582
H	PRO190
H	HOH524

site_id	AD3
Number of Residues	2
Details	binding site for residue CL F 402

Chain	Residue
E	GLY230
F	LYS308

site_id	AD4
Number of Residues	21
Details	binding site for residue NAD G 401

Chain	Residue
E	PRO190
G	GLY9
G	GLY11
G	ARG12
G	ILE13
G	ASN33
G	ASP34
G	LEU35
G	ASN77
G	PRO78
G	CYS96
G	THR97
G	GLY98
G	PHE99
G	PHE100
G	SER120
G	ALA121
G	CYS151
G	ASN315
G	TYR319
G	HOH511

site_id	AD5
Number of Residues	24
Details	binding site for residue NAD H 401

Chain	Residue
F	PRO190
H	GLY9
H	GLY11
H	ARG12
H	ILE13
H	ASN33
H	ASP34
H	LEU35
H	PRO78
H	CYS96
H	THR97
H	GLY98
H	PHE99
H	SER120
H	ALA121
H	CYS151
H	ASN315
H	TYR319
H	HOH502
H	HOH511
H	HOH515
H	HOH517
H	HOH522
H	HOH525

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ALA149-LEU156

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