Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4RFL

Crystal structure of G1PDH with NADPH from Methanocaldococcus jannaschii

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	THR100
A	THR101
A	SER103
A	ASN104
A	GLY106
A	SER113
A	SER137
A	PRO138
A	LEU141
A	HIS230
A	LYS37
A	HIS247
A	ZN403
A	EDO407
A	HOH501
A	HOH511
A	HOH521
A	HOH531
A	HOH592
A	HOH601
A	ASN38
A	THR39
A	TYR42
A	TYR52
A	GLY78
A	ARG79
A	ASP82

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

Chain	Residue
A	ASP105
A	ASP148
A	SER151
A	ASN152
A	ALA221

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

Chain	Residue
A	ASP148
A	HIS226
A	HIS247
A	NDP401
A	HOH501

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 404

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

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 405

Chain	Residue
A	ILE2
A	ILE3
B	ILE11

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

Chain	Residue
A	ILE11
B	ILE2
B	ILE3

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 407

Chain	Residue
A	SER118
A	SER218
A	SER222
A	HIS230
A	ARG310
A	NDP401
A	HOH513

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

Chain	Residue
A	LYS264
A	LEU328
A	GLU331

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 409

Chain	Residue
A	ARG139
A	TYR197

site_id	BC1
Number of Residues	29
Details	BINDING SITE FOR RESIDUE NDP B 401

Chain	Residue
B	GLY36
B	LYS37
B	ASN38
B	THR39
B	TYR52
B	GLY77
B	GLY78
B	ARG79
B	ASP82
B	THR100
B	THR101
B	SER103
B	ASN104
B	GLY106
B	SER113
B	SER137
B	PRO138
B	LEU141
B	HIS226
B	HIS230
B	HIS247
B	ZN403
B	HOH515
B	HOH540
B	HOH548
B	HOH556
B	HOH573
B	HOH578
B	HOH604

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K B 402

Chain	Residue
B	ASP105
B	ASP148
B	SER151
B	ASN152
B	ALA221

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 403

Chain	Residue
B	HIS226
B	HIS247
B	NDP401
B	HOH501
B	ASP148

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 404

Chain	Residue
B	LYS179
B	LYS183

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO B 405

Chain	Residue
B	CYS43
B	ARG44
B	PHE45
B	PHE46
B	HOH559
D	LEU194
D	LYS282
D	VAL283
D	ASP284

site_id	BC6
Number of Residues	24
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	ASP105
C	GLY106
C	ILE111
C	SER113
C	SER137
C	LEU141
C	HIS247
C	HOH501
C	HOH521
C	HOH553

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K C 402

Chain	Residue
C	ASP105
C	ASP148
C	SER151
C	ASN152
C	ALA221

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 403

Chain	Residue
C	ASP148
C	HIS226
C	HIS247
C	HOH501

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 404

Chain	Residue
C	ILE2
C	ILE3
D	ILE11

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 405

Chain	Residue
C	SER143
C	TYR197
C	VAL283

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 406

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

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 407

Chain	Residue
C	ILE11
D	ILE2

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA C 408

Chain	Residue
C	ARG7
C	TYR8
D	ILE125
D	HOH592

site_id	CC5
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NDP D 401

Chain	Residue
D	GLY36
D	LYS37
D	ASN38
D	THR39
D	TYR42
D	TYR52
D	GLY77
D	GLY78
D	ARG79
D	ASP82
D	THR100
D	SER103
D	ASN104
D	GLY106
D	SER113
D	GLN116
D	SER137
D	PRO138
D	LEU141
D	HIS230
D	HIS247
D	HOH501
D	HOH535
D	HOH538
D	HOH540
D	HOH573

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K D 402

Chain	Residue
D	ASP105
D	ASP148
D	SER151
D	ASN152
D	ALA221

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 403

Chain	Residue
D	ASP148
D	HIS226
D	HIS247
D	HOH501

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 404

Chain	Residue
B	LYS282
D	CYS43
D	ARG44
D	PHE45
D	PHE46

site_id	CC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 405

Chain	Residue
D	LYS203

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 406

Chain	Residue
D	LEU26
D	HOH527
D	HOH541

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)