Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4K9D

X-ray crystal structure of a Glyceraldehyde 3-phosphate dehydrogenase from Brugia malayi bound to the co-factor NAD

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
D	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006006	biological_process	glucose metabolic process
D	0006096	biological_process	glycolytic 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	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006006	biological_process	glucose metabolic process
E	0006096	biological_process	glycolytic 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	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006006	biological_process	glucose metabolic process
F	0006096	biological_process	glycolytic 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	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006006	biological_process	glucose metabolic process
G	0006096	biological_process	glycolytic 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	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006006	biological_process	glucose metabolic process
H	0006096	biological_process	glycolytic 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	30
Details	BINDING SITE FOR RESIDUE NAD A 401

Chain	Residue
A	ASN9
A	PHE37
A	ILE38
A	SER83
A	LYS84
A	SER102
A	THR103
A	GLY104
A	SER126
A	ALA127
A	CYS157
A	GLY10
A	ALA188
A	ASN321
A	TYR325
A	HOH502
A	HOH504
A	HOH510
A	HOH511
A	HOH574
A	HOH586
A	HOH594
A	PHE11
A	HOH628
A	GLY12
A	ARG13
A	ILE14
A	ASN34
A	ASP35
A	PRO36

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 402

Chain	Residue
A	PRO133
A	MET134
A	LYS224

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 403

Chain	Residue
A	ARG20
A	HIS53
A	GLY293
A	TYR323

site_id	AC4
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAD B 401

Chain	Residue
B	ASN9
B	GLY10
B	GLY12
B	ARG13
B	ILE14
B	ASP35
B	PRO36
B	PHE37
B	SER83
B	LYS84
B	SER102
B	THR103
B	GLY104
B	SER126
B	ALA127
B	CYS157
B	ALA188
B	ASN321
B	TYR325
B	HOH501
B	HOH502
B	HOH520
B	HOH521
B	HOH522
B	HOH523
B	HOH528
B	HOH550
B	HOH617
B	HOH618
B	HOH626
B	HOH642
B	HOH643
B	HOH660
B	HOH670

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 402

Chain	Residue
B	ARG20
B	HIS53
B	GLY293
B	TYR323

site_id	AC6
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAD C 401

Chain	Residue
C	HOH573
C	HOH587
C	HOH626
F	HOH617
C	ASN9
C	GLY10
C	GLY12
C	ARG13
C	ILE14
C	ASN34
C	ASP35
C	PRO36
C	PHE37
C	SER83
C	LYS84
C	SER102
C	THR103
C	GLY104
C	PHE106
C	SER126
C	ALA127
C	ALA188
C	ASN321
C	TYR325
C	HOH502
C	HOH521
C	HOH538
C	HOH540

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 402

Chain	Residue
C	ARG20
C	HIS53
C	TYR323
C	HOH543

site_id	AC8
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD D 500

Chain	Residue
D	ASN9
D	GLY10
D	PHE11
D	GLY12
D	ARG13
D	ILE14
D	ASN34
D	ASP35
D	PRO36
D	PHE37
D	ILE38
D	LYS84
D	SER102
D	THR103
D	GLY104
D	PHE106
D	SER126
D	ALA127
D	ALA188
D	ASN321
D	TYR325
D	HOH601
D	HOH602
D	HOH604
D	HOH605
D	HOH628
D	HOH661
D	HOH668
D	HOH669
D	HOH686
D	HOH687

site_id	AC9
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD E 500

Chain	Residue
E	ASN9
E	GLY10
E	GLY12
E	ARG13
E	ILE14
E	ASP35
E	PRO36
E	PHE37
E	LYS84
E	SER102
E	THR103
E	GLY104
E	SER126
E	CYS157
E	ALA188
E	ASN321
E	HOH622
E	HOH642
E	HOH658
H	PRO196

site_id	BC1
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAD F 401

Chain	Residue
F	ASN9
F	GLY10
F	GLY12
F	ARG13
F	ILE14
F	ASP35
F	PRO36
F	PHE37
F	SER83
F	LYS84
F	SER102
F	THR103
F	GLY104
F	SER126
F	ALA127
F	ALA188
F	ASN321
F	TYR325
F	HOH519
F	HOH521
F	HOH531
F	HOH532
F	HOH533
F	HOH547
F	HOH612
F	HOH616
F	HOH630
F	HOH642

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO F 402

Chain	Residue
F	ARG20
F	HIS53
F	GLY293

site_id	BC3
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAD G 401

Chain	Residue
G	ASN9
G	GLY10
G	PHE11
G	GLY12
G	ARG13
G	ILE14
G	ASN34
G	ASP35
G	PRO36
G	PHE37
G	LYS84
G	SER102
G	THR103
G	GLY104
G	PHE106
G	SER126
G	ALA127
G	ALA188
G	ASN321
G	TYR325
G	HOH522
G	HOH523
G	HOH537
G	HOH562
G	HOH564
G	HOH567
G	HOH611
G	HOH666
G	HOH668
G	HOH670

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO G 402

Chain	Residue
G	PRO133
G	MET134
G	LYS224
G	HOH648

site_id	BC5
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAD H 500

Chain	Residue
E	PRO196
H	ASN9
H	GLY12
H	ARG13
H	ILE14
H	ASP35
H	PRO36
H	PHE37
H	ILE38
H	LYS84
H	SER102
H	GLY104
H	SER126
H	ALA127
H	ALA188
H	ASN321
H	TYR325
H	HOH614

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	ALA155-LEU162

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Nucleophile => ECO:0000255\|PROSITE-ProRule:PRU10009

Chain	Residue	Details
A	CYS157
B	CYS157
C	CYS157
D	CYS157
E	CYS157
F	CYS157
G	CYS157
H	CYS157

site_id	SWS_FT_FI2
Number of Residues	64
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	ARG13
B	ASP35
B	LYS84
B	SER156
B	THR187
B	THR216
B	ARG239
B	ASN321
C	ARG13
C	ASP35
C	LYS84
A	ASP35
C	SER156
C	THR187
C	THR216
C	ARG239
C	ASN321
D	ARG13
D	ASP35
D	LYS84
D	SER156
D	THR187
A	LYS84
D	THR216
D	ARG239
D	ASN321
E	ARG13
E	ASP35
E	LYS84
E	SER156
E	THR187
E	THR216
E	ARG239
A	SER156
E	ASN321
F	ARG13
F	ASP35
F	LYS84
F	SER156
F	THR187
F	THR216
F	ARG239
F	ASN321
G	ARG13
A	THR187
G	ASP35
G	LYS84
G	SER156
G	THR187
G	THR216
G	ARG239
G	ASN321
H	ARG13
H	ASP35
H	LYS84
A	THR216
H	SER156
H	THR187
H	THR216
H	ARG239
H	ASN321
A	ARG239
A	ASN321
B	ARG13

site_id	SWS_FT_FI3
Number of Residues	8
Details	SITE: Activates thiol group during catalysis => ECO:0000250

Chain	Residue	Details
A	HIS184
B	HIS184
C	HIS184
D	HIS184
E	HIS184
F	HIS184
G	HIS184
H	HIS184

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