Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3PEF

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens in complex with NADP+

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0016054	biological_process	organic acid catabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
B	0000166	molecular_function	nucleotide binding
B	0016054	biological_process	organic acid catabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
C	0000166	molecular_function	nucleotide binding
C	0016054	biological_process	organic acid catabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
D	0000166	molecular_function	nucleotide binding
D	0016054	biological_process	organic acid catabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0050661	molecular_function	NADP binding
D	0051287	molecular_function	NAD binding
E	0000166	molecular_function	nucleotide binding
E	0016054	biological_process	organic acid catabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0050661	molecular_function	NADP binding
E	0051287	molecular_function	NAD binding
F	0000166	molecular_function	nucleotide binding
F	0016054	biological_process	organic acid catabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0050661	molecular_function	NADP binding
F	0051287	molecular_function	NAD binding
G	0000166	molecular_function	nucleotide binding
G	0016054	biological_process	organic acid catabolic process
G	0016491	molecular_function	oxidoreductase activity
G	0050661	molecular_function	NADP binding
G	0051287	molecular_function	NAD binding
H	0000166	molecular_function	nucleotide binding
H	0016054	biological_process	organic acid catabolic process
H	0016491	molecular_function	oxidoreductase activity
H	0050661	molecular_function	NADP binding
H	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAP A 301

Chain	Residue
A	LEU9
A	LEU65
A	ALA66
A	ALA70
A	GLU73
A	VAL74
A	THR96
A	VAL121
A	GLY123
A	SER124
A	ALA231
A	GLY10
A	PHE232
A	PRO233
A	HIS236
A	LYS239
A	GOL288
A	HOH296
A	HOH315
A	HOH333
A	HOH343
A	HOH362
A	ILE11
A	HOH456
A	HOH572
A	HOH1002
A	MET12
A	ASN31
A	ARG32
A	SER33
A	LYS36
A	MET64

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL A 288

Chain	Residue
A	GLY123
A	SER124
A	LYS171
A	ASN175
A	MET178
A	PHE232
A	NAP301
A	HOH479
A	HOH572
A	HOH635
A	HOH693

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 289

Chain	Residue
A	ASP67
A	LYS235
A	HIS236
A	LYS239
A	ARG242
A	ARG269

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 290

Chain	Residue
A	LEU203
A	GLY207
A	ALA212
A	ASN213
A	PHE216
A	ALA217

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG A 291

Chain	Residue
A	ALA246
A	ASP249
A	HOH307
D	ARG242
D	HOH311
D	HOH476

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 292

Chain	Residue
A	GLY106
A	VAL110
A	PHE116
A	VAL164
A	HOH293
A	HOH429
A	HOH662
A	HOH701

site_id	AC7
Number of Residues	27
Details	BINDING SITE FOR RESIDUE NAP B 301

Chain	Residue
B	LEU9
B	GLY10
B	ILE11
B	MET12
B	ASN31
B	ARG32
B	SER33
B	MET64
B	LEU65
B	ALA66
B	ALA70
B	GLU73
B	VAL74
B	THR96
B	VAL121
B	GLY123
B	SER124
B	ALA231
B	PHE232
B	PRO233
B	HIS236
B	LYS239
B	HOH311
B	HOH393
B	HOH500
B	HOH613
B	HOH626

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 288

Chain	Residue
G	HOH638
B	ARG141
G	NAP301
G	HOH493

site_id	AC9
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAP C 301

Chain	Residue
C	LEU9
C	GLY10
C	ILE11
C	MET12
C	ASN31
C	ARG32
C	SER33
C	LYS36
C	MET64
C	LEU65
C	ALA66
C	ALA70
C	GLU73
C	VAL74
C	THR96
C	VAL121
C	GLY123
C	SER124
C	ALA231
C	PHE232
C	PRO233
C	HIS236
C	LYS239
C	GOL288
C	HOH308
C	HOH317
C	HOH445
C	HOH450
C	HOH465
C	HOH582

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 288

Chain	Residue
C	GLY123
C	SER124
C	LYS171
C	ASN175
C	MET178
C	PHE232
C	NAP301

site_id	BC2
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAP D 301

Chain	Residue
D	LEU9
D	GLY10
D	ILE11
D	MET12
D	ASN31
D	ARG32
D	SER33
D	MET64
D	LEU65
D	ALA66
D	ALA70
D	GLU73
D	VAL74
D	THR96
D	VAL121
D	GLY123
D	SER124
D	ALA231
D	PHE232
D	PRO233
D	HIS236
D	LYS239
D	HOH303
D	HOH321
D	HOH324
D	HOH334
D	HOH584
D	HOH586
D	HOH730
D	HOH742
D	HOH922
D	HOH928
D	HOH1088

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG D 288

Chain	Residue
D	LEU203
D	GLY207
D	ALA212
D	ASN213
D	PHE216
D	ALA217

site_id	BC4
Number of Residues	29
Details	BINDING SITE FOR RESIDUE NAP E 301

Chain	Residue
E	LEU9
E	GLY10
E	ILE11
E	MET12
E	ASN31
E	ARG32
E	SER33
E	LYS36
E	MET64
E	LEU65
E	ALA66
E	ALA70
E	GLU73
E	VAL74
E	THR96
E	VAL121
E	GLY123
E	SER124
E	ALA231
E	PHE232
E	HIS236
E	LYS239
E	HOH310
E	HOH317
E	HOH336
E	HOH341
E	HOH481
E	HOH507
E	HOH589

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL E 288

Chain	Residue
C	ASP204
C	GLY207
C	ALA208
E	ARG32
E	SER33

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL E 289

Chain	Residue
E	LEU203
E	GLY207
E	ALA212
E	ASN213
E	ALA217

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG E 290

Chain	Residue
E	ALA246
E	ASP249
E	HOH299
E	HOH306
H	ARG242
H	HOH299

site_id	BC8
Number of Residues	27
Details	BINDING SITE FOR RESIDUE NAP F 301

Chain	Residue
F	LEU9
F	GLY10
F	ILE11
F	MET12
F	ASN31
F	ARG32
F	SER33
F	LYS36
F	MET64
F	LEU65
F	ALA66
F	ALA70
F	GLU73
F	VAL74
F	THR96
F	VAL121
F	GLY123
F	SER124
F	ALA231
F	PHE232
F	PRO233
F	HIS236
F	LYS239
F	HOH297
F	HOH593
F	HOH951
F	HOH1092

site_id	BC9
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAP G 301

Chain	Residue
B	GOL288
G	LEU9
G	GLY10
G	ILE11
G	MET12
G	ASN31
G	ARG32
G	SER33
G	MET64
G	LEU65
G	ALA66
G	ALA70
G	GLU73
G	VAL74
G	THR96
G	VAL121
G	GLY123
G	SER124
G	ALA231
G	PHE232
G	HIS236
G	LYS239
G	HOH309
G	HOH493
G	HOH597
G	HOH638
G	HOH878
G	HOH1094

site_id	CC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PEG G 288

Chain	Residue
A	ARG32
A	PRO34
A	HOH309
G	LEU203
G	ILE206
G	GLY207
G	ALA212
G	ASN213
G	PHE216
G	ALA217
G	HOH435
G	HOH839

site_id	CC2
Number of Residues	27
Details	BINDING SITE FOR RESIDUE NAP H 301

Chain	Residue
H	LEU9
H	GLY10
H	ILE11
H	MET12
H	ASN31
H	ARG32
H	SER33
H	LYS36
H	MET64
H	LEU65
H	ALA66
H	ALA70
H	GLU73
H	VAL74
H	THR96
H	GLY123
H	SER124
H	ALA231
H	PHE232
H	PRO233
H	HIS236
H	LYS239
H	HOH448
H	HOH508
H	HOH600
H	HOH686
H	HOH1098

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PEG H 288

Chain	Residue
H	LEU203
H	ILE206
H	GLY207
H	ALA212
H	ASN213
H	PHE216
H	ALA217

Functional Information from PROSITE/UniProt

site_id	PS00895
Number of Residues	14
Details	3_HYDROXYISOBUT_DH 3-hydroxyisobutyrate dehydrogenase signature. FIGLGiMGsaMAkN

Chain	Residue	Details
A	PHE6-ASN19

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