Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3RVD

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both 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	18
Details	BINDING SITE FOR RESIDUE NAD A 401

Chain	Residue
A	GLY7
A	PHE99
A	THR119
A	ALA120
A	CYS149
A	ASN313
A	TYR317
A	SO4402
A	HOH504
I	GLU72
A	GLY9
A	ARG10
A	ILE11
A	ASP32
A	ARG77
A	GLY95
A	THR96
A	GLY97

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 402

Chain	Residue
A	THR179
A	ASP181
A	ARG195
A	ARG231
A	NAD401

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 403

Chain	Residue
A	SER148
A	THR208
A	GLY209
A	ALA210
A	HOH515

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 404

Chain	Residue
Q	PHE251
Q	ALA252
Q	VAL299
Q	HOH523

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 405

Chain	Residue
A	ASN256
A	ARG260

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 406

Chain	Residue
A	ARG102
A	ASP124
A	HOH561

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 407

Chain	Residue
A	THR127
A	LEU216
A	HOH568

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 408

Chain	Residue
A	TYR137
A	SER138
A	HIS139
A	LYS333
A	HOH572

site_id	AC9
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD B 401

Chain	Residue
B	GLY7
B	PHE8
B	GLY9
B	ARG10
B	ILE11
B	THR33
B	ARG77
B	GLY95
B	THR96
B	GLY97
B	PHE99
B	THR119
B	ALA120
B	CYS149
B	THR179
B	ASN313
B	GLU314
J	TYR76
J	ASP77
J	ASN78

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 402

Chain	Residue
B	GLU253
B	ASN256
B	ARG260
B	HOH531
B	HOH535

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 403

Chain	Residue
B	PRO126
B	THR127
B	LEU216

site_id	BC3
Number of Residues	17
Details	BINDING SITE FOR RESIDUE NAD C 401

Chain	Residue
C	GLY7
C	PHE8
C	GLY9
C	ARG10
C	ILE11
C	ASP32
C	THR33
C	ARG77
C	GLY95
C	THR96
C	GLY97
C	PHE99
C	THR119
C	ALA120
C	CYS149
C	ASN313
C	SO4402

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 402

Chain	Residue
C	THR179
C	ASP181
C	ARG231
C	NAD401

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 403

Chain	Residue
C	HOH512
C	SER148
C	THR150
C	THR208
C	GLY209
C	ALA210

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 404

Chain	Residue
C	GLU253
C	ASN256
C	ARG260
E	GLU103

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 405

Chain	Residue
C	PRO126
C	THR127
C	LEU216

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 406

Chain	Residue
C	LYS122
C	HOH552
O	SER138
O	HIS139
O	ASP140
O	LYS333

site_id	BC9
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD D 401

Chain	Residue
D	GLY7
D	PHE8
D	GLY9
D	ARG10
D	ILE11
D	ASN31
D	ASP32
D	THR33
D	ARG77
D	GLY97
D	VAL98
D	THR119
D	ALA120
D	CYS149
D	ASN313
D	GLU314
D	TYR317
D	HOH508
I	GLU69
I	TYR76

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 402

Chain	Residue
D	GLU253
D	ASN256
D	ARG260
D	HOH550

site_id	CC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAD E 401

Chain	Residue
E	PHE8
E	GLY9
E	ARG10
E	ILE11
E	ASP32
E	ARG77
E	THR96
E	GLY97
E	PHE99
E	THR119
E	ALA120
E	CYS149
E	THR179
E	ASN313
E	TYR317
E	SO4402
H	SER188
N	GLU72

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 402

Chain	Residue
E	THR179
E	ASP181
E	ARG195
E	ARG231
E	NAD401

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 E 403

Chain	Residue
E	SER148
E	THR150
E	SER207
E	THR208
E	GLY209
E	ALA210

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 404

Chain	Residue
E	GLU253
E	ASN256
E	ARG260

site_id	CC6
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD F 401

Chain	Residue
F	GLY7
F	PHE8
F	GLY9
F	ARG10
F	ILE11
F	ASP32
F	THR33
F	ASN76
F	ARG77
F	GLY95
F	THR96
F	GLY97
F	VAL98
F	PHE99
F	THR119
F	ALA120
F	CYS149
F	ASN313
F	SO4402
G	SER188
M	GLU72

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 402

Chain	Residue
F	THR179
F	ARG195
F	ARG231
F	NAD401

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 403

Chain	Residue
F	SER148
F	THR150
F	THR208
F	ALA210

site_id	CC9
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAD G 401

Chain	Residue
F	SER188
G	GLY7
G	GLY9
G	ARG10
G	ILE11
G	ASN31
G	ASP32
G	THR33
G	ARG77
G	GLY95
G	THR96
G	GLY97
G	PHE99
G	THR119
G	ALA120
G	CYS149
G	ASN313
G	GLU314
G	TYR317
G	HOH506
G	HOH507
M	TYR76
M	ASP77

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 G 402

Chain	Residue
G	GLU253
G	ASN256
G	ARG260
G	SER294

site_id	DC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD H 401

Chain	Residue
E	SER188
H	GLY7
H	PHE8
H	GLY9
H	ARG10
H	ILE11
H	ASN31
H	ASP32
H	THR33
H	ARG77
H	GLY95
H	GLY97
H	THR119
H	ALA120
H	CYS149
H	THR179
H	ASN313
H	GLU314
H	TYR317
H	HOH505
N	GLU69
N	TYR76

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 H 402

Chain	Residue
H	GLU253
H	ASN256
H	ARG260
H	SER294

site_id	DC4
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAD O 401

Chain	Residue
K	GLU69
K	TYR76
K	HOH103
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	CYS149
O	SER188
O	ASN313
O	TYR317
O	HOH506
O	HOH521
O	HOH571

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 O 402

Chain	Residue
O	GLU253
O	ASN256
O	ARG260

site_id	DC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 O 403

Chain	Residue
O	ARG194
Q	SER295
Q	LEU296

site_id	DC7
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NAD Q 401

Chain	Residue
L	GLU69
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	ASN313
Q	TYR317
Q	SO4402

site_id	DC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 Q 402

Chain	Residue
Q	THR179
Q	ASP181
Q	ARG195
Q	NAD401
Q	HOH528

site_id	DC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 Q 403

Chain	Residue
Q	SER148
Q	THR150
Q	THR208
Q	GLY209
Q	ALA210
Q	HOH518
Q	HOH537
Q	HOH559

site_id	EC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 Q 404

Chain	Residue
Q	ILE125
Q	PRO126
Q	THR127
Q	LEU216

site_id	EC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 Q 405

Chain	Residue
O	HOH561

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)