Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3PDU

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter sulfurreducens 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	36
Details	BINDING SITE FOR RESIDUE NAP A 301

Chain	Residue
A	GLY8
A	LEU65
A	ALA66
A	ALA70
A	GLU73
A	VAL74
A	THR96
A	VAL121
A	GLY123
A	THR124
A	LYS125
A	LEU9
A	LYS171
A	SER231
A	PHE232
A	PRO233
A	HIS236
A	LYS239
A	HOH308
A	HOH310
A	HOH325
A	HOH362
A	GLY10
A	HOH437
A	HOH560
A	HOH630
A	HOH740
A	HOH1011
A	HOH1186
A	HOH1423
A	ILE11
A	MET12
A	ASN31
A	ARG32
A	ASN33
A	MET64

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 304

Chain	Residue
A	ARG250
A	HOH410
B	ARG242
B	GLU246

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 304

Chain	Residue
A	ARG242
A	GLU246
A	HOH754
B	ARG250
B	HOH1791
B	HOH1797

site_id	AC4
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAP B 301

Chain	Residue
B	GLY8
B	LEU9
B	GLY10
B	ILE11
B	MET12
B	ASN31
B	ARG32
B	ASN33
B	MET64
B	LEU65
B	ALA66
B	ALA70
B	GLU73
B	VAL74
B	THR96
B	VAL121
B	GLY123
B	THR124
B	SER231
B	PHE232
B	HIS236
B	LYS239
B	HOH292
B	HOH296
B	HOH317
B	HOH555
B	HOH564
B	HOH603
B	HOH918
B	HOH925
B	HOH1116
B	HOH1534
B	HOH1589

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 305

Chain	Residue
B	GLY131
B	GLY155
B	LYS156
B	HOH303
B	HOH312
B	HOH539
B	HOH541
B	HOH760

site_id	AC6
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAP C 301

Chain	Residue
C	GLU73
C	VAL74
C	THR96
C	VAL121
C	GLY123
C	THR124
C	LYS171
C	SER231
C	PHE232
C	HIS236
C	LYS239
C	HOH297
C	HOH314
C	HOH818
C	HOH971
C	HOH1099
C	HOH1102
C	HOH1510
C	HOH1557
C	HOH1567
C	GLY8
C	LEU9
C	GLY10
C	ILE11
C	MET12
C	ASN31
C	ARG32
C	ASN33
C	MET64
C	LEU65
C	ALA66
C	ALA70

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 304

Chain	Residue
C	ARG242
C	GLU246
C	HOH474
D	ARG250

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

Chain	Residue
C	ARG250
C	HOH581
D	ARG242
D	GLU246

site_id	AC9
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAP D 301

Chain	Residue
D	GLY8
D	LEU9
D	GLY10
D	ILE11
D	MET12
D	ASN31
D	ARG32
D	ASN33
D	LYS36
D	MET64
D	LEU65
D	ALA66
D	ALA70
D	GLU73
D	VAL74
D	THR96
D	VAL121
D	GLY123
D	THR124
D	LYS171
D	SER231
D	PHE232
D	PRO233
D	HIS236
D	LYS239
D	HOH296
D	HOH312
D	HOH316
D	HOH339
D	HOH554
D	HOH800
D	HOH938
D	HOH1097
D	HOH1439

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 305

Chain	Residue
D	GLU227
D	PHE228
D	PRO229
D	GLU276
D	HOH656
F	ALA52
F	ASN79

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

Chain	Residue
E	GLY8
E	LEU9
E	GLY10
E	ILE11
E	MET12
E	ASN31
E	ARG32
E	ASN33
E	MET64
E	LEU65
E	ALA66
E	ALA70
E	GLU73
E	VAL74
E	THR96
E	VAL121
E	GLY123
E	THR124
E	SER231
E	PHE232
E	PRO233
E	HIS236
E	LYS239
E	HOH317
E	HOH451
E	HOH913
E	HOH1016
E	HOH1081
E	HOH1109
E	HOH1132
E	HOH1284
E	HOH1498
E	HOH1598

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 304

Chain	Residue
E	ARG242
E	GLU246
E	HOH1345
G	GLU246
G	ARG250
G	HOH717

site_id	BC4
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAP F 301

Chain	Residue
F	GLY8
F	LEU9
F	GLY10
F	ILE11
F	MET12
F	ASN31
F	ARG32
F	ASN33
F	MET64
F	LEU65
F	ALA66
F	ALA70
F	GLU73
F	VAL74
F	THR96
F	VAL121
F	GLY123
F	THR124
F	SER231
F	PHE232
F	PRO233
F	HIS236
F	LYS239
F	HOH292
F	HOH293
F	HOH339
F	HOH348
F	HOH350
F	HOH456
F	HOH466
F	HOH478
F	HOH617
F	HOH779
F	HOH1009
F	HOH1021

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL F 304

Chain	Residue
F	ARG242
F	GLU246
F	HOH766
H	ARG250

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL F 288

Chain	Residue
F	GLU246
F	ARG250
F	HOH1104
H	ARG242
H	GLU246
H	HOH330

site_id	BC7
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAP G 301

Chain	Residue
G	GLY8
G	LEU9
G	GLY10
G	ILE11
G	MET12
G	ASN31
G	ARG32
G	ASN33
G	MET64
G	LEU65
G	ALA66
G	ALA70
G	GLU73
G	VAL74
G	THR96
G	VAL121
G	GLY123
G	THR124
G	LYS171
G	SER231
G	PHE232
G	PRO233
G	HIS236
G	LYS239
G	HOH294
G	HOH593
G	HOH857
G	HOH1495

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL G 304

Chain	Residue
E	ARG250
E	HOH1178
G	ARG242
G	GLU246

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL H 305

Chain	Residue
B	HOH541
B	HOH773
H	ASN19
H	ASP130
H	ALA152
H	ALA153
H	HOH477
H	HOH540
H	HOH1018

site_id	CC1
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAP H 301

Chain	Residue
H	GLY8
H	LEU9
H	GLY10
H	ILE11
H	MET12
H	ASN31
H	ARG32
H	ASN33
H	MET64
H	LEU65
H	ALA66
H	ALA70
H	GLU73
H	VAL74
H	THR96
H	VAL121
H	GLY123
H	THR124
H	SER231
H	PHE232
H	PRO233
H	HIS236
H	LYS239
H	HOH314
H	HOH319
H	HOH321
H	HOH322
H	HOH325
H	HOH331
H	HOH395
H	HOH484
H	HOH759
H	HOH876
H	HOH1064
H	HOH1206

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	PHE6-ASN19

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