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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VG6

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0051287	molecular_function	NAD binding
B	0000166	molecular_function	nucleotide binding
B	0051287	molecular_function	NAD binding
C	0000166	molecular_function	nucleotide binding
C	0051287	molecular_function	NAD binding
D	0000166	molecular_function	nucleotide binding
D	0051287	molecular_function	NAD binding
E	0000166	molecular_function	nucleotide binding
E	0051287	molecular_function	NAD binding
F	0000166	molecular_function	nucleotide binding
F	0051287	molecular_function	NAD binding
G	0000166	molecular_function	nucleotide binding
G	0051287	molecular_function	NAD binding
H	0000166	molecular_function	nucleotide binding
H	0051287	molecular_function	NAD binding
I	0000166	molecular_function	nucleotide binding
I	0051287	molecular_function	NAD binding
J	0000166	molecular_function	nucleotide binding
J	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	38
Details	binding site for residue NDP A 401

Chain	Residue
A	ARG96
A	ARG174
A	THR175
A	MET204
A	LEU205
A	PRO206
A	GLU210
A	VAL232
A	ALA233
A	ARG234
A	ASP258
A	MET106
A	HIS282
A	ALA284
A	SER285
A	TYR319
A	MES402
A	HOH501
A	HOH520
A	HOH540
A	HOH549
A	HOH551
A	LEU151
A	HOH554
A	HOH584
A	HOH604
A	HOH616
A	HOH636
A	HOH654
A	HOH713
A	HOH724
A	HOH747
A	GLY152
A	ASP153
A	LEU154
A	GLY155
A	TRP172
A	SER173

site_id	AC2
Number of Residues	11
Details	binding site for residue MES A 402

Chain	Residue
A	VAL15
A	ASP16
A	TRP57
A	GLY77
A	ALA78
A	GLY79
A	ARG234
A	HIS282
A	NDP401
A	HOH560
A	HOH652

site_id	AC3
Number of Residues	7
Details	binding site for residue MES A 403

Chain	Residue
A	ARG174
A	THR175
A	LEU188
A	HOH548
C	ASP153
C	ALA156
C	ALA157

site_id	AC4
Number of Residues	36
Details	binding site for residue NDP B 401

Chain	Residue
B	ALA78
B	ARG96
B	MET106
B	LEU151
B	GLY152
B	ASP153
B	LEU154
B	GLY155
B	TRP172
B	SER173
B	ARG174
B	THR175
B	LYS177
B	MET204
B	LEU205
B	PRO206
B	GLU210
B	THR211
B	VAL232
B	ARG234
B	ASP258
B	HIS282
B	ALA284
B	SER285
B	TYR319
B	MES402
B	HOH504
B	HOH512
B	HOH525
B	HOH531
B	HOH535
B	HOH552
B	HOH563
B	HOH568
B	HOH611
B	HOH630

site_id	AC5
Number of Residues	12
Details	binding site for residue MES B 402

Chain	Residue
B	ARG234
B	HIS282
B	NDP401
B	HOH529
C	HOH502
B	VAL15
B	ASP16
B	TRP57
B	LEU76
B	GLY77
B	ALA78
B	GLY79

site_id	AC6
Number of Residues	38
Details	binding site for residue NDP C 401

Chain	Residue
A	ARG316
A	HOH516
A	HOH523
C	ARG96
C	MET106
C	GLY150
C	LEU151
C	GLY152
C	ASP153
C	LEU154
C	GLY155
C	TRP172
C	SER173
C	ARG174
C	THR175
C	LYS177
C	MET204
C	LEU205
C	PRO206
C	VAL232
C	ALA233
C	ARG234
C	ASP258
C	HIS282
C	ALA284
C	SER285
C	TYR319
C	MES402
C	HOH513
C	HOH526
C	HOH536
C	HOH584
C	HOH594
C	HOH603
C	HOH621
C	HOH641
C	HOH668
C	HOH689

site_id	AC7
Number of Residues	9
Details	binding site for residue MES C 402

Chain	Residue
C	VAL15
C	ASP16
C	TRP57
C	LEU76
C	GLY77
C	ALA78
C	GLY79
C	ARG234
C	NDP401

site_id	AC8
Number of Residues	25
Details	binding site for residue NDP D 401

Chain	Residue
D	ARG96
D	MET106
D	GLY150
D	LEU151
D	GLY152
D	ASP153
D	LEU154
D	TRP172
D	SER173
D	ARG174
D	THR175
D	MET204
D	LEU205
D	PRO206
D	VAL232
D	ALA233
D	ARG234
D	ASP258
D	HIS282
D	ALA284
D	SER285
D	TYR319
D	MES402
D	HOH501
D	HOH527

site_id	AC9
Number of Residues	9
Details	binding site for residue MES D 402

Chain	Residue
D	ASP16
D	TRP57
D	GLY77
D	ALA78
D	GLY79
D	ARG234
D	HIS282
D	NDP401
D	HOH541

site_id	AD1
Number of Residues	42
Details	binding site for residue NDP E 401

Chain	Residue
E	ALA78
E	ARG96
E	MET106
E	GLY150
E	LEU151
E	GLY152
E	ASP153
E	LEU154
E	GLY155
E	TRP172
E	SER173
E	ARG174
E	THR175
E	MET204
E	LEU205
E	PRO206
E	GLU210
E	THR211
E	VAL232
E	ALA233
E	ARG234
E	ASP258
E	HIS282
E	ALA284
E	SER285
E	TYR319
E	MES402
E	HOH508
E	HOH517
E	HOH530
E	HOH534
E	HOH540
E	HOH547
E	HOH558
E	HOH569
E	HOH578
E	HOH595
E	HOH605
E	HOH611
E	HOH616
E	HOH635
E	HOH654

site_id	AD2
Number of Residues	8
Details	binding site for residue MES E 402

Chain	Residue
E	ASP16
E	TRP57
E	GLY77
E	ALA78
E	GLY79
E	ARG234
E	HIS282
E	NDP401

site_id	AD3
Number of Residues	27
Details	binding site for residue NDP F 401

Chain	Residue
F	ARG96
F	MET106
F	GLY150
F	LEU151
F	GLY152
F	ASP153
F	LEU154
F	GLY155
F	TRP172
F	SER173
F	ARG174
F	THR175
F	MET204
F	LEU205
F	PRO206
F	THR211
F	VAL232
F	ALA233
F	ARG234
F	ASP258
F	HIS282
F	ALA284
F	SER285
F	TYR319
F	MES402
F	HOH501
F	HOH530

site_id	AD4
Number of Residues	9
Details	binding site for residue MES F 402

Chain	Residue
F	ASP16
F	TRP57
F	LEU76
F	GLY77
F	ALA78
F	GLY79
F	ARG234
F	HIS282
F	NDP401

site_id	AD5
Number of Residues	29
Details	binding site for residue NDP G 401

Chain	Residue
G	ARG96
G	MET106
G	LEU151
G	GLY152
G	ASP153
G	LEU154
G	GLY155
G	TRP172
G	SER173
G	ARG174
G	THR175
G	MET204
G	LEU205
G	PRO206
G	GLU210
G	THR211
G	VAL232
G	ALA233
G	ARG234
G	ASP258
G	VAL259
G	HIS282
G	ALA284
G	SER285
G	TYR319
G	HOH515
G	HOH524
G	HOH539
G	HOH541

site_id	AD6
Number of Residues	26
Details	binding site for residue NDP H 401

Chain	Residue
H	ALA78
H	GLY79
H	ARG96
H	MET106
H	LEU151
H	GLY152
H	ASP153
H	LEU154
H	TRP172
H	SER173
H	ARG174
H	THR175
H	LEU205
H	PRO206
H	THR211
H	VAL232
H	ALA233
H	ARG234
H	ASP258
H	HIS282
H	ALA284
H	SER285
H	TYR319
H	HOH502
H	HOH506
H	HOH525

site_id	AD7
Number of Residues	38
Details	binding site for residue NDP I 401

Chain	Residue
I	ALA78
I	ARG96
I	MET106
I	LEU151
I	GLY152
I	ASP153
I	LEU154
I	GLY155
I	TRP172
I	SER173
I	ARG174
I	THR175
I	LYS177
I	MET204
I	LEU205
I	PRO206
I	VAL232
I	ALA233
I	ARG234
I	ASP258
I	HIS282
I	ALA284
I	SER285
I	TYR319
I	MES402
I	HOH507
I	HOH508
I	HOH528
I	HOH551
I	HOH595
I	HOH605
I	HOH629
I	HOH633
I	HOH652
I	HOH740
I	HOH745
J	ARG316
J	HOH502

site_id	AD8
Number of Residues	8
Details	binding site for residue MES I 402

Chain	Residue
I	ASP16
I	TRP57
I	ALA78
I	GLY79
I	ARG234
I	HIS282
I	NDP401
I	HOH717

site_id	AD9
Number of Residues	38
Details	binding site for residue NDP J 401

Chain	Residue
J	ARG96
J	MET106
J	LEU151
J	GLY152
J	ASP153
J	LEU154
J	GLY155
J	TRP172
J	SER173
J	ARG174
J	THR175
J	MET204
J	LEU205
J	PRO206
J	GLU210
J	VAL232
J	ALA233
J	ARG234
J	ASP258
J	HIS282
J	ALA284
J	SER285
J	TYR319
J	MES402
J	HOH510
J	HOH516
J	HOH540
J	HOH544
J	HOH559
J	HOH580
J	HOH586
J	HOH587
J	HOH597
J	HOH625
J	HOH631
J	HOH650
J	HOH662
J	HOH742

site_id	AE1
Number of Residues	12
Details	binding site for residue MES J 402

Chain	Residue
J	VAL15
J	ASP16
J	TRP57
J	GLY77
J	ALA78
J	GLY79
J	ARG234
J	HIS282
J	NDP401
J	HOH553
J	HOH616
J	HOH730

223166

PDB entries from 2024-07-31

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