Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4RGQ

Crystal structure of the Methanocaldococcus jannaschii G1PDH with NADPH and DHAP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0006629	biological_process	lipid metabolic process
A	0006650	biological_process	glycerophospholipid metabolic process
A	0008654	biological_process	phospholipid biosynthetic process
A	0008888	molecular_function	glycerol dehydrogenase (NAD+) activity
A	0016491	molecular_function	oxidoreductase activity
A	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
A	0046872	molecular_function	metal ion binding
A	0050492	molecular_function	glycerol-1-phosphate dehydrogenase [NAD(P)+] activity
A	0106357	molecular_function	glycerol-1-phosphate dehydrogenase (NAD+) activity
A	0106358	molecular_function	glycerol-1-phosphate dehydrogenase (NADP+) activity
B	0005737	cellular_component	cytoplasm
B	0006629	biological_process	lipid metabolic process
B	0006650	biological_process	glycerophospholipid metabolic process
B	0008654	biological_process	phospholipid biosynthetic process
B	0008888	molecular_function	glycerol dehydrogenase (NAD+) activity
B	0016491	molecular_function	oxidoreductase activity
B	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
B	0046872	molecular_function	metal ion binding
B	0050492	molecular_function	glycerol-1-phosphate dehydrogenase [NAD(P)+] activity
B	0106357	molecular_function	glycerol-1-phosphate dehydrogenase (NAD+) activity
B	0106358	molecular_function	glycerol-1-phosphate dehydrogenase (NADP+) activity
C	0005737	cellular_component	cytoplasm
C	0006629	biological_process	lipid metabolic process
C	0006650	biological_process	glycerophospholipid metabolic process
C	0008654	biological_process	phospholipid biosynthetic process
C	0008888	molecular_function	glycerol dehydrogenase (NAD+) activity
C	0016491	molecular_function	oxidoreductase activity
C	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
C	0046872	molecular_function	metal ion binding
C	0050492	molecular_function	glycerol-1-phosphate dehydrogenase [NAD(P)+] activity
C	0106357	molecular_function	glycerol-1-phosphate dehydrogenase (NAD+) activity
C	0106358	molecular_function	glycerol-1-phosphate dehydrogenase (NADP+) activity
D	0005737	cellular_component	cytoplasm
D	0006629	biological_process	lipid metabolic process
D	0006650	biological_process	glycerophospholipid metabolic process
D	0008654	biological_process	phospholipid biosynthetic process
D	0008888	molecular_function	glycerol dehydrogenase (NAD+) activity
D	0016491	molecular_function	oxidoreductase activity
D	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
D	0046872	molecular_function	metal ion binding
D	0050492	molecular_function	glycerol-1-phosphate dehydrogenase [NAD(P)+] activity
D	0106357	molecular_function	glycerol-1-phosphate dehydrogenase (NAD+) activity
D	0106358	molecular_function	glycerol-1-phosphate dehydrogenase (NADP+) activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NDP A 401

Chain	Residue
A	GLY36
A	THR101
A	SER103
A	ASN104
A	GLY106
A	SER109
A	ILE111
A	SER113
A	SER137
A	PRO138
A	LEU141
A	LYS37
A	HIS247
A	13P404
A	HOH510
A	HOH520
A	HOH529
A	HOH536
A	HOH570
A	HOH635
A	HOH637
A	ASN38
A	THR39
A	TYR52
A	GLY78
A	ARG79
A	ASP82
A	THR100

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

Chain	Residue
A	ASP105
A	ASP148
A	ASN152
A	ALA221
A	13P404

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

Chain	Residue
A	ASP105
A	ASP148
A	HIS226
A	HIS247
A	13P404

site_id	AC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE 13P A 404

Chain	Residue
A	ASP105
A	GLN116
A	SER118
A	SER218
A	ALA221
A	SER222
A	HIS226
A	HIS230
A	HIS247
A	ARG310
A	NDP401
A	K402
A	ZN403
A	HOH543
A	HOH637

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 405

Chain	Residue
A	ILE3
A	VAL4
A	PRO110
A	VAL121
A	ALA123
A	ALA213
A	ASN216

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO A 406

Chain	Residue
A	LYS85
A	ALA88
A	TYR89
A	PHE95
A	VAL121
A	ASP122
A	ALA123
A	PRO124
A	HOH502
A	HOH579

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 407

Chain	Residue
A	ASN17
A	ILE19
A	GLU20
A	TYR47
A	HOH508
A	HOH530
A	HOH611
B	SER270

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 408

Chain	Residue
A	ARG139
A	SER143
A	HOH617

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 409

Chain	Residue
A	LYS90
A	LEU91
A	GLY92

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 410

Chain	Residue
A	PRO138
C	GLU274

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 411

Chain	Residue
A	TYR260
A	LYS264
A	GLU324
A	GLU331

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 412

Chain	Residue
A	ILE2
A	ILE3
B	ILE11

site_id	BC4
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NDP B 401

Chain	Residue
B	GLY77
B	GLY78
B	ARG79
B	ASP82
B	THR100
B	THR101
B	SER103
B	ASN104
B	GLY106
B	SER109
B	ILE111
B	SER113
B	SER137
B	LEU141
B	HIS247
B	1GP404
B	HOH506
B	HOH518
B	HOH533
B	HOH547
B	GLY36
B	LYS37
B	ASN38
B	THR39
B	TYR42
B	TYR52

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K B 402

Chain	Residue
B	ASP105
B	ASP148
B	ASN152
B	ALA221
B	1GP404

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 403

Chain	Residue
B	ASP105
B	ASP148
B	HIS226
B	HIS247
B	1GP404

site_id	BC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE 1GP B 404

Chain	Residue
B	ASP105
B	SER113
B	GLN116
B	SER118
B	ASP148
B	SER218
B	ALA221
B	SER222
B	HIS226
B	HIS230
B	ARG310
B	NDP401
B	K402
B	ZN403

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 405

Chain	Residue
B	CYS43
B	ARG44
B	PHE45
B	HOH606
D	LYS282
D	VAL283
D	ASP284

site_id	BC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 406

Chain	Residue
B	ILE3
B	VAL4
B	PRO110
B	MET120
B	VAL121
B	ALA123
B	ALA213
B	ASN216

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 407

Chain	Residue
B	LYS264
B	GLU324
B	GLU331

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 408

Chain	Residue
B	LEU26
B	HOH604
B	HOH618

site_id	CC3
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NDP C 401

Chain	Residue
C	GLY36
C	LYS37
C	ASN38
C	THR39
C	TYR42
C	TYR52
C	GLY77
C	GLY78
C	ARG79
C	ASP82
C	THR100
C	THR101
C	SER103
C	ASN104
C	GLY106
C	ILE111
C	SER113
C	SER137
C	LEU141
C	HIS247
C	13P404
C	HOH537

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K C 402

Chain	Residue
C	ASP105
C	ASP148
C	ASN152
C	ALA221
C	13P404

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 403

Chain	Residue
C	ASP148
C	HIS226
C	HIS247
C	13P404
C	HOH501

site_id	CC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE 13P C 404

Chain	Residue
C	ASP105
C	SER118
C	ASP148
C	SER218
C	ALA221
C	SER222
C	HIS226
C	HIS230
C	HIS247
C	ARG310
C	NDP401
C	K402
C	ZN403
C	HOH501
C	HOH527
C	HOH580

site_id	CC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 405

Chain	Residue
C	SER143
C	VAL283

site_id	CC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 406

Chain	Residue
C	GLU168
C	SER217

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 407

Chain	Residue
C	ILE2
D	ILE10
D	ILE11
D	HOH597

site_id	DC1
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NDP D 401

Chain	Residue
D	GLY36
D	LYS37
D	ASN38
D	THR39
D	TYR52
D	GLY77
D	GLY78
D	ARG79
D	ASP82
D	THR100
D	THR101
D	SER103
D	ASN104
D	GLY106
D	SER109
D	ILE111
D	SER113
D	SER137
D	PRO138
D	LEU141
D	HIS247
D	13P404
D	HOH501
D	HOH516
D	HOH520
D	HOH540
D	HOH543
D	HOH560

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K D 402

Chain	Residue
D	ASP105
D	ASP148
D	ASN152
D	ALA221
D	13P404

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 403

Chain	Residue
D	ASP105
D	ASP148
D	HIS226
D	HIS247
D	13P404
D	HOH501

site_id	DC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE 13P D 404

Chain	Residue
D	ASP105
D	SER113
D	SER118
D	SER218
D	ALA221
D	SER222
D	HIS226
D	HIS230
D	HIS247
D	ARG310
D	NDP401
D	K402
D	ZN403
D	HOH501
D	HOH525

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 405

Chain	Residue
B	LYS282
B	VAL283
B	ASP284
D	CYS43
D	ARG44
D	PHE45

site_id	DC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 406

Chain	Residue
D	ILE3
D	VAL4
D	PRO110
D	VAL121
D	ALA123
D	ALA213
D	ASN216

site_id	DC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 407

Chain	Residue
D	LYS179
D	HOH594

site_id	DC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 408

Chain	Residue
D	LYS203

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	52
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00497","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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