Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5FB3

Structure of glycerophosphate dehydrogenase in complex with NADPH

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue ZN A 2001

Chain	Residue
A	ASP157
A	HIS238
A	HIS256

site_id	AC2
Number of Residues	5
Details	binding site for residue SO4 A 2002

Chain	Residue
A	PHE117
A	SER230
A	SER234
A	HIS242
A	ARG312

site_id	AC3
Number of Residues	3
Details	binding site for residue SO4 A 2003

Chain	Residue
A	GLY127
A	LYS128
A	TYR92

site_id	AC4
Number of Residues	4
Details	binding site for residue SO4 A 2004

Chain	Residue
A	ILE60
A	VAL65
A	GLU66
A	LYS69

site_id	AC5
Number of Residues	3
Details	binding site for residue ZN B 2001

Chain	Residue
B	ASP157
B	HIS238
B	HIS256

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 B 2002

Chain	Residue
B	ARG173
B	HOH2104
D	TRP275

site_id	AC7
Number of Residues	4
Details	binding site for residue SO4 B 2003

Chain	Residue
B	PRO70
B	GLY71
B	PHE72
B	LYS96

site_id	AC8
Number of Residues	6
Details	binding site for residue PPV B 2004

Chain	Residue
B	GLY80
B	GLY81
B	ARG82
B	SER106
B	LEU150
B	HOH2108

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN C 2001

Chain	Residue
C	ASP108
C	ASP157
C	HIS238
C	HIS256

site_id	AD1
Number of Residues	5
Details	binding site for residue SO4 C 2002

Chain	Residue
C	PHE117
C	SER230
C	SER234
C	HIS242
C	ARG312

site_id	AD2
Number of Residues	5
Details	binding site for residue SO4 C 2003

Chain	Residue
C	GLU5
C	TYR179
C	SER180
C	GLU181
D	LYS215

site_id	AD3
Number of Residues	29
Details	binding site for residue NDP D 1001

Chain	Residue
D	GLY38
D	LYS39
D	SER40
D	SER41
D	THR42
D	GLY80
D	GLY81
D	ARG82
D	PRO83
D	ASP85
D	THR103
D	SER104
D	SER106
D	HIS107
D	ASP108
D	TYR114
D	VAL115
D	SER116
D	LEU119
D	ILE142
D	SER145
D	LEU150
D	GLU251
D	HIS256
D	HOH1101
D	HOH1111
D	HOH1113
D	HOH1129
F	ARG206

site_id	AD4
Number of Residues	4
Details	binding site for residue ZN D 1002

Chain	Residue
D	ASP108
D	ASP157
D	HIS238
D	HIS256

site_id	AD5
Number of Residues	4
Details	binding site for residue SO4 D 1003

Chain	Residue
D	SER290
D	ARG292
D	GLN293
F	ARG149

site_id	AD6
Number of Residues	22
Details	binding site for residue NDP E 1001

Chain	Residue
E	SER145
E	ALA146
E	LEU150
E	HIS256
E	HOH1102
E	GLY38
E	LYS39
E	SER40
E	SER41
E	THR42
E	GLY80
E	GLY81
E	ARG82
E	ASP85
E	THR103
E	SER104
E	SER106
E	HIS107
E	TYR114
E	VAL115
E	SER116
E	ILE142

site_id	AD7
Number of Residues	3
Details	binding site for residue ZN E 1002

Chain	Residue
E	ASP157
E	HIS238
E	HIS256

site_id	AD8
Number of Residues	5
Details	binding site for residue SO4 E 1003

Chain	Residue
E	GLY228
E	SER229
E	SER230
E	ARG312
E	ARG315

site_id	AD9
Number of Residues	3
Details	binding site for residue SO4 F 401

Chain	Residue
C	ARG166
C	GLY272
F	ARG166

site_id	AE1
Number of Residues	25
Details	binding site for residue NDP F 402

Chain	Residue
F	GLY38
F	LYS39
F	SER40
F	SER41
F	THR42
F	GLY80
F	GLY81
F	ARG82
F	ASP85
F	THR103
F	SER106
F	HIS107
F	TYR114
F	VAL115
F	SER116
F	ILE142
F	SER145
F	ALA146
F	LEU150
F	GLU251
F	HIS256
F	HOH506
F	HOH518
F	HOH519
F	HOH534

site_id	AE2
Number of Residues	4
Details	binding site for residue ZN F 403

Chain	Residue
F	ASP157
F	HIS238
F	HIS256
F	HOH527

site_id	AE3
Number of Residues	5
Details	binding site for residue SO4 F 404

Chain	Residue
D	LYS202
D	ASN203
F	SER41
F	LYS44
F	HOH505

site_id	AE4
Number of Residues	5
Details	binding site for residue SO4 F 405

Chain	Residue
F	PRO70
F	GLY71
F	HIS94
F	LYS96
F	HOH517

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	78
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)