Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5NUF

Cytosolic Malate Dehydrogenase 1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000325	cellular_component	plant-type vacuole
A	0003729	molecular_function	mRNA binding
A	0003824	molecular_function	catalytic activity
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005794	cellular_component	Golgi apparatus
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006099	biological_process	tricarboxylic acid cycle
A	0006108	biological_process	malate metabolic process
A	0009506	cellular_component	plasmodesma
A	0009507	cellular_component	chloroplast
A	0009570	cellular_component	chloroplast stroma
A	0010043	biological_process	response to zinc ion
A	0016491	molecular_function	oxidoreductase activity
A	0016615	molecular_function	malate dehydrogenase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0019752	biological_process	carboxylic acid metabolic process
A	0030060	molecular_function	L-malate dehydrogenase (NAD+) activity
A	0048046	cellular_component	apoplast
B	0000325	cellular_component	plant-type vacuole
B	0003729	molecular_function	mRNA binding
B	0003824	molecular_function	catalytic activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005794	cellular_component	Golgi apparatus
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006099	biological_process	tricarboxylic acid cycle
B	0006108	biological_process	malate metabolic process
B	0009506	cellular_component	plasmodesma
B	0009507	cellular_component	chloroplast
B	0009570	cellular_component	chloroplast stroma
B	0010043	biological_process	response to zinc ion
B	0016491	molecular_function	oxidoreductase activity
B	0016615	molecular_function	malate dehydrogenase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0019752	biological_process	carboxylic acid metabolic process
B	0030060	molecular_function	L-malate dehydrogenase (NAD+) activity
B	0048046	cellular_component	apoplast
C	0000325	cellular_component	plant-type vacuole
C	0003729	molecular_function	mRNA binding
C	0003824	molecular_function	catalytic activity
C	0005515	molecular_function	protein binding
C	0005576	cellular_component	extracellular region
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005794	cellular_component	Golgi apparatus
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006099	biological_process	tricarboxylic acid cycle
C	0006108	biological_process	malate metabolic process
C	0009506	cellular_component	plasmodesma
C	0009507	cellular_component	chloroplast
C	0009570	cellular_component	chloroplast stroma
C	0010043	biological_process	response to zinc ion
C	0016491	molecular_function	oxidoreductase activity
C	0016615	molecular_function	malate dehydrogenase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0019752	biological_process	carboxylic acid metabolic process
C	0030060	molecular_function	L-malate dehydrogenase (NAD+) activity
C	0048046	cellular_component	apoplast

Functional Information from PDB Data

site_id	AC1
Number of Residues	33
Details	binding site for residue NAD A 401

Chain	Residue
A	GLY12
A	GLY90
A	PHE91
A	PRO92
A	ILE109
A	GLN113
A	VAL130
A	ALA131
A	ASN132
A	LEU156
A	HIS188
A	ALA14
A	SER243
A	SO4403
A	HOH510
A	HOH516
A	HOH525
A	HOH539
A	HOH557
A	HOH560
A	HOH562
A	HOH566
A	GLY15
A	HOH580
A	HOH595
A	HOH610
A	HOH644
A	GLN16
A	ILE17
A	ASP43
A	ILE44
A	VAL88
A	GLY89

site_id	AC2
Number of Residues	8
Details	binding site for residue SO4 A 402

Chain	Residue
A	ARG7
A	ILE38
A	HIS40
A	VAL70
A	HOH641
B	GLU170
B	HOH509
B	HOH520

site_id	AC3
Number of Residues	8
Details	binding site for residue SO4 A 403

Chain	Residue
A	ASN132
A	ARG163
A	HIS188
A	GLY232
A	SER243
A	NAD401
A	HOH531
A	HOH584

site_id	AC4
Number of Residues	6
Details	binding site for residue SO4 A 404

Chain	Residue
A	ALA122
A	PRO123
A	ASN124
A	HOH583
B	ARG171
B	GLU223

site_id	AC5
Number of Residues	4
Details	binding site for residue GOL A 405

Chain	Residue
A	ALA14
A	GLY15
A	ARG239
A	HOH571

site_id	AC6
Number of Residues	5
Details	binding site for residue GOL A 406

Chain	Residue
A	SER277
A	TYR278
A	GLN301
A	GLY302
A	PEG408

site_id	AC7
Number of Residues	4
Details	binding site for residue PEO A 407

Chain	Residue
A	THR73
A	HOH513
A	HOH528
C	HOH582

site_id	AC8
Number of Residues	5
Details	binding site for residue PEG A 408

Chain	Residue
A	TYR278
A	LEU303
A	ARG310
A	GOL406
A	HOH526

site_id	AC9
Number of Residues	3
Details	binding site for residue NA A 409

Chain	Residue
A	ASP217
A	ASP221
A	HOH688

site_id	AD1
Number of Residues	5
Details	binding site for residue NA A 410

Chain	Residue
A	ASP275
A	SER277
A	GLN301
A	HOH650
A	HOH680

site_id	AD2
Number of Residues	1
Details	binding site for residue EDO A 411

Chain	Residue
A	LEU260

site_id	AD3
Number of Residues	4
Details	binding site for residue EDO A 412

Chain	Residue
A	ASP221
A	SER226
A	GLN229
A	LYS312

site_id	AD4
Number of Residues	4
Details	binding site for residue EDO A 413

Chain	Residue
A	ILE59
A	GLN167
A	ARG231
A	HOH607

site_id	AD5
Number of Residues	4
Details	binding site for residue EDO A 414

Chain	Residue
A	SER169
A	GLU170
A	VAL174
A	HOH534

site_id	AD6
Number of Residues	30
Details	binding site for residue NAD B 401

Chain	Residue
B	ASP43
B	ILE44
B	VAL88
B	GLY89
B	GLY90
B	PRO92
B	ILE109
B	GLN113
B	VAL130
B	ALA131
B	ASN132
B	LEU156
B	HIS188
B	SER243
B	SO4402
B	HOH519
B	HOH527
B	HOH544
B	HOH556
B	HOH567
B	HOH568
B	HOH575
B	HOH580
B	HOH586
B	HOH597
B	GLY12
B	ALA14
B	GLY15
B	GLN16
B	ILE17

site_id	AD7
Number of Residues	7
Details	binding site for residue SO4 B 402

Chain	Residue
B	ASN132
B	ARG163
B	HIS188
B	GLY232
B	SER243
B	NAD401
B	HOH587

site_id	AD8
Number of Residues	3
Details	binding site for residue SO4 B 403

Chain	Residue
B	ARG7
B	HIS40
B	VAL70

site_id	AD9
Number of Residues	3
Details	binding site for residue ACT B 404

Chain	Residue
B	GLU322
B	ASP325
B	HOH542

site_id	AE1
Number of Residues	6
Details	binding site for residue GOL B 405

Chain	Residue
B	ARG239
B	HOH505
B	HOH564
C	ALA14
C	GLY15
C	GLN16

site_id	AE2
Number of Residues	6
Details	binding site for residue GOL B 406

Chain	Residue
B	GLN167
B	ARG231
B	HOH503
B	HOH576
C	MET56
C	ILE59

site_id	AE3
Number of Residues	2
Details	binding site for residue FMT B 407

Chain	Residue
B	GLU150
B	HOH638

site_id	AE4
Number of Residues	3
Details	binding site for residue NA B 408

Chain	Residue
B	GLU170
B	HOH652
C	HOH660

site_id	AE5
Number of Residues	1
Details	binding site for residue EDO B 409

Chain	Residue
B	LEU260

site_id	AE6
Number of Residues	31
Details	binding site for residue NAD C 401

Chain	Residue
C	GLY12
C	ALA14
C	GLY15
C	GLN16
C	ILE17
C	ASP43
C	ILE44
C	VAL88
C	GLY89
C	GLY90
C	PHE91
C	PRO92
C	ASN106
C	ILE109
C	GLN113
C	VAL130
C	ASN132
C	LEU156
C	HIS188
C	SER242
C	SO4403
C	ACT405
C	HOH505
C	HOH515
C	HOH544
C	HOH562
C	HOH564
C	HOH583
C	HOH605
C	HOH608
C	HOH611

site_id	AE7
Number of Residues	5
Details	binding site for residue SO4 C 402

Chain	Residue
A	GLU170
C	ARG7
C	ILE38
C	HIS40
C	HOH543

site_id	AE8
Number of Residues	11
Details	binding site for residue SO4 C 403

Chain	Residue
C	ARG93
C	ARG99
C	ASN132
C	ARG163
C	HIS188
C	GLY232
C	SER243
C	NAD401
C	HOH546
C	HOH549
C	HOH606

site_id	AE9
Number of Residues	9
Details	binding site for residue SO4 C 404

Chain	Residue
C	GLU98
C	ARG99
C	SER189
C	SER190
C	GLN230
C	HOH519
C	HOH525
C	HOH627
C	HOH633

site_id	AF1
Number of Residues	7
Details	binding site for residue ACT C 405

Chain	Residue
C	PRO92
C	ARG93
C	ILE236
C	SER242
C	NAD401
C	HOH546
C	HOH606

site_id	AF2
Number of Residues	8
Details	binding site for residue GOL C 406

Chain	Residue
B	ILE299
B	VAL300
B	GLN301
C	LYS100
C	ASP101
C	MET103
C	SER104
C	HOH545

site_id	AF3
Number of Residues	3
Details	binding site for residue GOL C 407

Chain	Residue
C	GLN167
C	ARG231
C	HOH512

site_id	AF4
Number of Residues	4
Details	binding site for residue GOL C 408

Chain	Residue
C	SER277
C	TYR278
C	GLN301
C	GLY302

site_id	AF5
Number of Residues	6
Details	binding site for residue GOL C 409

Chain	Residue
C	GLU118
C	ALA122
C	ASN124
C	CYS125
C	HOH504
C	HOH602

site_id	AF6
Number of Residues	5
Details	binding site for residue GOL C 410

Chain	Residue
C	LYS142
C	PRO146
C	ILE148
C	PRO149
C	GLU150

site_id	AF7
Number of Residues	3
Details	binding site for residue PEO C 411

Chain	Residue
C	SER108
C	LYS111
C	SER332

site_id	AF8
Number of Residues	3
Details	binding site for residue EDO C 412

Chain	Residue
C	ASP216
C	ASP217
C	ALA218

site_id	AF9
Number of Residues	2
Details	binding site for residue EDO C 413

Chain	Residue
C	ARG239
C	HOH506

Functional Information from PROSITE/UniProt

site_id	PS00068
Number of Residues	13
Details	MDH Malate dehydrogenase active site signature. LTRLDhnRAlgqI

Chain	Residue	Details
A	LEU156-ILE168

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: Proton acceptor => ECO:0000250\|UniProtKB:P11708

Chain	Residue	Details
A	HIS188
B	HIS188
C	HIS188

site_id	SWS_FT_FI2
Number of Residues	27
Details	BINDING: BINDING => ECO:0000269\|PubMed:29194485, ECO:0007744\|PDB:5NUE, ECO:0007744\|PDB:5NUF

Chain	Residue	Details
A	GLN16
B	GLN16
B	ASP43
B	GLY90
B	ARG99
B	GLN113
B	ASN132
B	ARG163
B	HIS188
B	SER243
C	GLN16
A	ASP43
C	ASP43
C	GLY90
C	ARG99
C	GLN113
C	ASN132
C	ARG163
C	HIS188
C	SER243
A	GLY90
A	ARG99
A	GLN113
A	ASN132
A	ARG163
A	HIS188
A	SER243

site_id	SWS_FT_FI3
Number of Residues	6
Details	MOD_RES: Methionine sulfoxide => ECO:0000269\|PubMed:29194485

Chain	Residue	Details
A	MET56
A	MET97
B	MET56
B	MET97
C	MET56
C	MET97

site_id	SWS_FT_FI4
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:19292762

Chain	Residue	Details
A	LYS119
B	LYS119
C	LYS119

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