Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1GD1

STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.8 ANGSTROMS RESOLUTION

Functional Information from GO Data

Chain	GOid	namespace	contents
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	ABO
Number of Residues	3
Details	RESIDUES IN CHAIN O WHICH INTERACT WITH THE ADENINE BASE OF NAD

Chain	Residue
O	LEU33
O	THR96
O	ARG77

site_id	ABP
Number of Residues	3
Details	RESIDUES IN CHAIN P WHICH INTERACT WITH THE ADENINE BASE OF NAD

Chain	Residue
P	LEU33
P	THR96
P	ARG77

site_id	ABQ
Number of Residues	3
Details	RESIDUES IN CHAIN Q WHICH INTERACT WITH THE ADENINE BASE OF NAD

Chain	Residue
Q	LEU33
Q	THR96
Q	ARG77

site_id	ABR
Number of Residues	3
Details	RESIDUES IN CHAIN R WHICH INTERACT WITH THE ADENINE BASE OF NAD

Chain	Residue
R	LEU33
R	THR96
R	ARG77

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 O 338

Chain	Residue
O	THR179
O	ASP181
O	ARG195
O	ARG231
O	NAD336
O	HOH349
O	HOH424
O	HOH443

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 O 339

Chain	Residue
O	SER148
O	THR208
O	GLY209
O	ALA210
O	HOH347
O	HOH391
O	HOH424
O	HOH440
O	HOH500

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 P 338

Chain	Residue
P	THR179
P	ASP181
P	ARG195
P	ARG231
P	NAD336
P	HOH355
P	HOH423
P	HOH442
P	HOH457

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 P 339

Chain	Residue
P	SER148
P	THR208
P	GLY209
P	ALA210
P	HOH353
P	HOH392
P	HOH439

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 Q 338

Chain	Residue
Q	HOH435
Q	THR179
Q	ASP181
Q	ARG195
Q	ARG231
Q	NAD336
Q	HOH358

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 Q 339

Chain	Residue
Q	SER148
Q	THR208
Q	GLY209
Q	ALA210
Q	HOH356
Q	HOH399
Q	HOH435
Q	HOH450
Q	HOH499

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 R 338

Chain	Residue
R	THR179
R	ASP181
R	ARG195
R	ARG231
R	NAD336
R	HOH360
R	HOH431
R	HOH450
R	HOH462

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 R 339

Chain	Residue
R	SER148
R	THR208
R	GLY209
R	HOH358
R	HOH399
R	HOH431
R	HOH447
R	HOH502

site_id	AC9
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD O 336

Chain	Residue
O	GLY7
O	GLY9
O	ARG10
O	ILE11
O	ASN31
O	ASP32
O	LEU33
O	ARG77
O	SER95
O	THR96
O	GLY97
O	PHE99
O	SER119
O	ALA120
O	CYS149
O	ASN180
O	ASN313
O	TYR317
O	SO4338
O	HOH349
O	HOH350
O	HOH352
O	HOH362
O	HOH363
O	HOH374
O	HOH380
O	HOH382
O	HOH403
O	HOH417
O	HOH456
R	HOH341

site_id	APO
Number of Residues	2
Details	RESIDUES IN CHAIN O WHICH INTERACT WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF NAD

Chain	Residue
O	ARG10
O	ASN180

site_id	APP
Number of Residues	2
Details	RESIDUES IN CHAIN P WHICH INTERACT WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF NAD

Chain	Residue
P	ARG10
P	ASN180

site_id	APQ
Number of Residues	2
Details	RESIDUES IN CHAIN Q WHICH INTERACT WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF NAD

Chain	Residue
Q	ARG10
Q	ASN180

site_id	APR
Number of Residues	2
Details	RESIDUES IN CHAIN R WHICH INTERACT WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF NAD

Chain	Residue
R	ARG10
R	ASN180

site_id	ARO
Number of Residues	1
Details	RESIDUES IN CHAIN O WHICH INTERACT WITH THE ADENOSINE RIBOSE OF NAD

Chain	Residue
O	ASP32

site_id	ARP
Number of Residues	1
Details	RESIDUES IN CHAIN P WHICH INTERACT WITH THE ADENOSINE RIBOSE OF NAD

Chain	Residue
P	ASP32

site_id	ARQ
Number of Residues	1
Details	RESIDUES IN CHAIN Q WHICH INTERACT WITH THE ADENOSINE RIBOSE OF NAD

Chain	Residue
Q	ASP32

site_id	ARR
Number of Residues	1
Details	RESIDUES IN CHAIN R WHICH INTERACT WITH THE ADENOSINE RIBOSE OF NAD

Chain	Residue
R	ASP32

site_id	BC1
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAD P 336

Chain	Residue
P	GLY7
P	PHE8
P	GLY9
P	ARG10
P	ILE11
P	ASN31
P	ASP32
P	LEU33
P	ARG77
P	SER95
P	THR96
P	GLY97
P	ARG98
P	PHE99
P	SER119
P	ALA120
P	CYS149
P	ASN180
P	ASN313
P	TYR317
P	SO4338
P	HOH355
P	HOH356
P	HOH358
P	HOH368
P	HOH369
P	HOH378
P	HOH382
P	HOH384
P	HOH404
P	HOH405
P	HOH417
P	HOH453
Q	LEU187
Q	HOH344

site_id	BC2
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD Q 336

Chain	Residue
Q	GLY7
Q	PHE8
Q	GLY9
Q	ARG10
Q	ILE11
Q	ASN31
Q	ASP32
Q	LEU33
Q	ARG77
Q	SER95
Q	THR96
Q	GLY97
Q	PHE99
Q	SER119
Q	ALA120
Q	CYS149
Q	ASN180
Q	ASN313
Q	TYR317
Q	SO4338
Q	HOH358
Q	HOH359
Q	HOH361
Q	HOH371
Q	HOH372
Q	HOH376
Q	HOH383
Q	HOH388
Q	HOH390
Q	HOH412
Q	HOH413
Q	HOH427
Q	HOH463

site_id	BC3
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD R 336

Chain	Residue
O	HOH512
R	GLY7
R	PHE8
R	GLY9
R	ARG10
R	ILE11
R	ASN31
R	ASP32
R	LEU33
R	ARG77
R	SER95
R	THR96
R	GLY97
R	SER119
R	ALA120
R	CYS149
R	ASN180
R	ASN313
R	TYR317
R	SO4338
R	HOH360
R	HOH361
R	HOH363
R	HOH372
R	HOH373
R	HOH383
R	HOH389
R	HOH391
R	HOH410
R	HOH411
R	HOH425
R	HOH459

site_id	CTO
Number of Residues	2
Details	RESIDUES IN CHAIN O INVOLVED IN CATALYSIS

Chain	Residue
O	CYS149
O	HIS176

site_id	CTP
Number of Residues	2
Details	RESIDUES IN CHAIN P INVOLVED IN CATALYSIS

Chain	Residue
P	CYS149
P	HIS176

site_id	CTQ
Number of Residues	2
Details	RESIDUES IN CHAIN Q INVOLVED IN CATALYSIS

Chain	Residue
Q	CYS149
Q	HIS176

site_id	CTR
Number of Residues	2
Details	RESIDUES IN CHAIN R INVOLVED IN CATALYSIS

Chain	Residue
R	CYS149
R	HIS176

site_id	NBO
Number of Residues	5
Details	RESIDUES OF CHAIN O WHICH INTERACT WITH THE NICOTINAMIDE BASE OF NAD

Chain	Residue
O	ILE11
O	CYS149
O	SER119
O	ASN313
O	TYR317

site_id	NBP
Number of Residues	5
Details	RESIDUES OF CHAIN P WHICH INTERACT WITH THE NICOTINAMIDE BASE OF NAD

Chain	Residue
P	ILE11
P	CYS149
P	SER119
P	ASN313
P	TYR317

site_id	NBQ
Number of Residues	5
Details	RESIDUES OF CHAIN Q WHICH INTERACT WITH THE NICOTINAMIDE BASE OF NAD

Chain	Residue
Q	ILE11
Q	CYS149
Q	SER119
Q	ASN313
Q	TYR317

site_id	NBR
Number of Residues	5
Details	RESIDUES OF CHAIN R WHICH INTERACT WITH THE NICOTINAMIDE BASE OF NAD

Chain	Residue
R	ILE11
R	CYS149
R	SER119
R	ASN313
R	TYR317

site_id	NPO
Number of Residues	1
Details	RESIDUES OF CHAIN O WHICH INTERACT WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
O	ILE11

site_id	NPP
Number of Residues	1
Details	RESIDUES OF CHAIN P WHICH INTERACT WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
P	ILE11

site_id	NPQ
Number of Residues	1
Details	RESIDUES OF CHAIN Q WHICH INTERACT WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
Q	ILE11

site_id	NPR
Number of Residues	1
Details	RESIDUES OF CHAIN R WHICH INTERACT WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
R	ILE11

site_id	NRO
Number of Residues	1
Details	RESIDUES OF CHAIN O WHICH INTERACT WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
O	SER119

site_id	NRP
Number of Residues	1
Details	RESIDUES OF CHAIN P WHICH INTERACT WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
P	SER119

site_id	NRQ
Number of Residues	1
Details	RESIDUES OF CHAIN Q WHICH INTERACT WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
Q	SER119

site_id	NRR
Number of Residues	1
Details	RESIDUES OF CHAIN R WHICH INTERACT WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF NAD

Chain	Residue
R	SER119

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	ALA147-LEU154

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Nucleophile => ECO:0000269\|PubMed:18480053, ECO:0000305\|PubMed:12569100

Chain	Residue	Details
O	THR150
P	THR150
Q	THR150
R	THR150

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:12569100, ECO:0000269\|PubMed:18480053, ECO:0000269\|PubMed:3586018, ECO:0000269\|PubMed:9175858

Chain	Residue	Details
O	ILE11
P	ALA120
P	ASP181
P	GLU314
Q	ILE11
Q	LEU33
Q	ASP78
Q	ALA120
Q	ASP181
Q	GLU314
R	ILE11
O	LEU33
R	LEU33
R	ASP78
R	ALA120
R	ASP181
R	GLU314
O	ASP78
O	ALA120
O	ASP181
O	GLU314
P	ILE11
P	LEU33
P	ASP78

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:12569100, ECO:0000269\|PubMed:18480053, ECO:0000269\|PubMed:3210237, ECO:0000269\|PubMed:3586018, ECO:0000269\|PubMed:9175858

Chain	Residue	Details
O	CYS149
R	CYS149
R	ASN180
R	VAL232
O	ASN180
O	VAL232
P	CYS149
P	ASN180
P	VAL232
Q	CYS149
Q	ASN180
Q	VAL232

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:12569100, ECO:0000269\|PubMed:18480053, ECO:0000269\|PubMed:9175858

Chain	Residue	Details
O	ALA196
P	ALA196
Q	ALA196
R	ALA196

site_id	SWS_FT_FI5
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:18480053, ECO:0000269\|PubMed:3210237, ECO:0000269\|PubMed:3586018, ECO:0000269\|PubMed:9175858

Chain	Residue	Details
O	GLY209
P	GLY209
Q	GLY209
R	GLY209

site_id	SWS_FT_FI6
Number of Residues	4
Details	SITE: Activates thiol group during catalysis => ECO:0000250\|UniProtKB:Q6GIL8

Chain	Residue	Details
O	SER177
P	SER177
Q	SER177
R	SER177

Catalytic Information from CSA

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

Chain	Residue	Details
O	CYS149
O	HIS176

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

Chain	Residue	Details
P	CYS149
P	HIS176

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

Chain	Residue	Details
Q	CYS149
Q	HIS176

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

Chain	Residue	Details
R	CYS149
R	HIS176

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