Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3K2B

Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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	0006006	biological_process	glucose metabolic process
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
O	0006006	biological_process	glucose metabolic process
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
Q	0006006	biological_process	glucose metabolic process
Q	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Q	0050661	molecular_function	NADP binding
Q	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD A 335

Chain	Residue
A	GLY7
A	THR96
A	GLY97
A	VAL98
A	PHE99
A	THR119
A	ALA120
A	CYS149
A	ASN313
A	TYR317
A	SO4336
A	PHE8
A	HOH343
A	HOH345
A	GLY9
A	ARG10
A	ILE11
A	ASP32
A	THR33
A	ARG77
A	GLY95

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 336

Chain	Residue
A	THR179
A	ASP181
A	ARG195
A	ARG231
A	NAD335

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 337

Chain	Residue
A	SER148
A	THR208
A	GLY209
A	ALA210

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 334

Chain	Residue
A	ARG20
A	LYS21
A	HOH800

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 338

Chain	Residue
A	ARG102
A	ASP124
A	HOH372
A	HOH373

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 339

Chain	Residue
A	PHE251
A	ALA252
A	GLU253
A	VAL299

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 340

Chain	Residue
A	GLU253
A	ASN256
A	ARG260
A	HOH865

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 341

Chain	Residue
A	SER138
A	HIS139
A	HOH706
A	HOH783

site_id	AC9
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAD B 335

Chain	Residue
B	GLY7
B	PHE8
B	GLY9
B	ARG10
B	ILE11
B	ASN31
B	ARG77
B	GLY95
B	THR96
B	GLY97
B	PHE99
B	THR119
B	ALA120
B	CYS149
B	ASN313
B	TYR317
B	SO4336
B	HOH354

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 336

Chain	Residue
B	THR179
B	ASP181
B	ARG195
B	NAD335
B	HOH874

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 337

Chain	Residue
B	SER148
B	THR150
B	THR208
B	GLY209
B	ALA210
B	HOH784
B	HOH874

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 334

Chain	Residue
B	ARG102
B	LYS122
B	GLY123
B	ASP124

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 338

Chain	Residue
B	SER138
B	HIS139
B	ASP140
B	ASN331

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 339

Chain	Residue
B	GLU253
B	ASN256
B	ARG260

site_id	BC6
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD C 335

Chain	Residue
C	THR96
C	GLY97
C	PHE99
C	THR119
C	ALA120
C	CYS149
C	ASN313
C	TYR317
C	SO4336
C	HOH349
C	HOH376
C	GLY7
C	PHE8
C	GLY9
C	ARG10
C	ILE11
C	ASP32
C	THR33
C	ARG77
C	GLY95

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 336

Chain	Residue
C	THR179
C	ASP181
C	ARG231
C	NAD335
C	HOH388

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 337

Chain	Residue
C	SER148
C	THR208
C	GLY209
C	ALA210

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 334

Chain	Residue
C	SER138
C	HIS139
C	ASN331

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 338

Chain	Residue
C	ASN256
C	ARG260
C	HOH412
C	HOH413

site_id	CC2
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD D 335

Chain	Residue
D	GLY7
D	PHE8
D	GLY9
D	ARG10
D	ILE11
D	ASP32
D	THR33
D	ASN76
D	ARG77
D	THR96
D	GLY97
D	THR119
D	ALA120
D	CYS149
D	ASN313
D	TYR317
D	SO4336
D	HOH365
D	HOH366
D	HOH377

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 336

Chain	Residue
D	THR179
D	ASP181
D	ARG231
D	NAD335

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 337

Chain	Residue
D	SER148
D	CYS149
D	THR150
D	THR208
D	ARG231
D	HOH399

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 334

Chain	Residue
D	GLU253
D	ASN256
D	ARG260

site_id	CC6
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NAD E 335

Chain	Residue
E	GLY7
E	PHE8
E	GLY9
E	ARG10
E	ILE11
E	ASN31
E	THR33
E	ARG77
E	GLY95
E	THR96
E	GLY97
E	THR119
E	ALA120
E	CYS149
E	THR179
E	ASN313
E	GLU314
E	TYR317
E	SO4336

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 336

Chain	Residue
E	THR179
E	ASP181
E	ARG195
E	ARG231
E	NAD335

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 337

Chain	Residue
E	SER148
E	THR150
E	THR208
E	GLY209
E	ALA210

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 334

Chain	Residue
E	GLU253
E	ASN256
E	ARG260
E	SER294
E	HOH536

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 338

Chain	Residue
E	ASP135
E	ILE327
E	ASN331

site_id	DC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE NAD F 335

Chain	Residue
F	GLY7
F	GLY9
F	ARG10
F	ILE11
F	ASP32
F	ARG77
F	GLY95
F	THR96
F	GLY97
F	VAL98
F	PHE99
F	THR119
F	ALA120
F	CYS149
F	ASN313
F	TYR317
G	SER188

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 336

Chain	Residue
F	THR179
F	ASP181
F	ARG195
F	ARG231

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 F 337

Chain	Residue
F	SER148
F	THR150
F	THR208
F	GLY209
F	ALA210

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 334

Chain	Residue
F	GLU253
F	ASN256
F	ARG260
F	ASP275

site_id	DC6
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NAD G 335

Chain	Residue
G	GLY7
G	GLY9
G	ARG10
G	ILE11
G	ASP32
G	THR33
G	ARG77
G	THR96
G	GLY97
G	PHE99
G	THR119
G	ALA120
G	CYS149
G	THR179
G	ASN313
G	GLU314
G	TYR317
G	SO4336
G	HOH340

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 G 336

Chain	Residue
G	THR179
G	ASP181
G	ARG195
G	ARG231
G	NAD335

site_id	DC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 G 337

Chain	Residue
G	SER148
G	THR150
G	THR208
G	GLY209
G	ALA210

site_id	DC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 G 334

Chain	Residue
G	THR127
G	LEU216

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 G 338

Chain	Residue
G	SER138
G	HIS139
G	ASP140

site_id	EC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 G 339

Chain	Residue
G	GLU253
G	ASN256
G	ARG260
G	HOH344
G	HOH652

site_id	EC3
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD H 335

Chain	Residue
E	SER188
H	GLY7
H	PHE8
H	GLY9
H	ARG10
H	ILE11
H	ASP32
H	THR33
H	ARG77
H	GLY95
H	THR96
H	GLY97
H	VAL98
H	THR119
H	ALA120
H	CYS149
H	THR179
H	ASN313
H	GLU314
H	TYR317
H	SO4336

site_id	EC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 H 336

Chain	Residue
H	THR179
H	ASP181
H	ARG195
H	ARG231
H	NAD335

site_id	EC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 H 337

Chain	Residue
H	SER148
H	THR150
H	SER207
H	THR208
H	ALA210
H	HOH861
H	HOH862

site_id	EC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 H 334

Chain	Residue
H	GLU253
H	ASN256
H	ARG260
H	SER294

site_id	EC7
Number of Residues	25
Details	BINDING SITE FOR RESIDUE NAD O 335

Chain	Residue
O	GLY7
O	PHE8
O	GLY9
O	ARG10
O	ILE11
O	ASP32
O	THR33
O	ARG77
O	GLY95
O	THR96
O	GLY97
O	PHE99
O	THR119
O	ALA120
O	ASN313
O	TYR317
O	SO4336
O	HOH346
O	HOH359
O	HOH362
O	HOH370
O	HOH434
O	HOH435
O	HOH436
O	HOH440

site_id	EC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 O 336

Chain	Residue
O	HOH35
O	THR179
O	ASP181
O	ARG195
O	ARG231
O	NAD335
O	HOH398
O	HOH415

site_id	EC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 O 337

Chain	Residue
O	SER148
O	THR150
O	THR208
O	ALA210
O	HOH397
O	HOH407
O	HOH857

site_id	FC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 O 334

Chain	Residue
O	GLY60
O	GLU61
O	THR62
O	HOH375

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 O 338

Chain	Residue
O	ARG102
O	LYS122
O	GLY123
O	ASP124

site_id	FC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 O 339

Chain	Residue
C	LYS122
O	SER138
O	HIS139
O	ASP140
O	LYS333
O	HOH409

site_id	FC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 O 340

Chain	Residue
O	GLU253
O	ASN256
O	ARG260

site_id	FC5
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD Q 335

Chain	Residue
Q	GLY7
Q	PHE8
Q	GLY9
Q	ARG10
Q	ILE11
Q	ASP32
Q	THR33
Q	ARG77
Q	GLY95
Q	THR96
Q	GLY97
Q	PHE99
Q	THR119
Q	ALA120
Q	CYS149
Q	THR179
Q	ASN313
Q	TYR317
Q	SO4336
Q	HOH346
Q	HOH350
Q	HOH446

site_id	FC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 Q 336

Chain	Residue
Q	THR179
Q	ASP181
Q	ARG195
Q	ARG231
Q	NAD335

site_id	FC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 Q 337

Chain	Residue
Q	SER148
Q	THR150
Q	THR208
Q	GLY209
Q	ALA210
Q	HOH467
Q	HOH790

site_id	FC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 Q 334

Chain	Residue
Q	PRO126
Q	THR127
Q	TYR128
Q	ASN133
Q	LEU216
Q	HOH462

site_id	FC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 Q 338

Chain	Residue
Q	PHE251
Q	ALA252
Q	VAL299
Q	HOH477

site_id	GC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 Q 339

Chain	Residue
Q	ARG284
Q	HOH805

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	ALA147-LEU154

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	10
Details	ACT_SITE: Nucleophile => ECO:0000255\|PROSITE-ProRule:PRU10009

Chain	Residue	Details
A	CYS149
Q	CYS149
B	CYS149
C	CYS149
D	CYS149
E	CYS149
F	CYS149
G	CYS149
H	CYS149
O	CYS149

site_id	SWS_FT_FI2
Number of Residues	40
Details	BINDING: BINDING => ECO:0000269\|PubMed:20516587, ECO:0000269\|PubMed:22514274

Chain	Residue	Details
A	ARG10
C	ASP32
C	ARG77
C	ASN313
D	ARG10
D	ASP32
D	ARG77
D	ASN313
E	ARG10
E	ASP32
E	ARG77
A	ASP32
E	ASN313
F	ARG10
F	ASP32
F	ARG77
F	ASN313
G	ARG10
G	ASP32
G	ARG77
G	ASN313
H	ARG10
A	ARG77
H	ASP32
H	ARG77
H	ASN313
O	ARG10
O	ASP32
O	ARG77
O	ASN313
Q	ARG10
Q	ASP32
Q	ARG77
A	ASN313
Q	ASN313
B	ARG10
B	ASP32
B	ARG77
B	ASN313
C	ARG10

site_id	SWS_FT_FI3
Number of Residues	50
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	SER148
B	ARG231
C	SER148
C	THR179
C	ARG195
C	THR208
C	ARG231
D	SER148
D	THR179
D	ARG195
D	THR208
A	THR179
D	ARG231
E	SER148
E	THR179
E	ARG195
E	THR208
E	ARG231
F	SER148
F	THR179
F	ARG195
F	THR208
A	ARG195
F	ARG231
G	SER148
G	THR179
G	ARG195
G	THR208
G	ARG231
H	SER148
H	THR179
H	ARG195
H	THR208
A	THR208
H	ARG231
O	SER148
O	THR179
O	ARG195
O	THR208
O	ARG231
Q	SER148
Q	THR179
Q	ARG195
Q	THR208
A	ARG231
Q	ARG231
B	SER148
B	THR179
B	ARG195
B	THR208

site_id	SWS_FT_FI4
Number of Residues	10
Details	SITE: Activates thiol group during catalysis => ECO:0000250

Chain	Residue	Details
A	HIS176
Q	HIS176
B	HIS176
C	HIS176
D	HIS176
E	HIS176
F	HIS176
G	HIS176
H	HIS176
O	HIS176

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