Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5NUE

Cytosolic Malate Dehydrogenase 1 (peroxide-treated)

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	0006107	biological_process	oxaloacetate metabolic process
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	0019674	biological_process	NAD+ metabolic process
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	0006107	biological_process	oxaloacetate metabolic process
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	0019674	biological_process	NAD+ metabolic process
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	0006107	biological_process	oxaloacetate metabolic process
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	0019674	biological_process	NAD+ metabolic process
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	PHE91
A	PRO92
A	ILE109
A	GLN113
A	VAL130
A	ALA131
A	ASN132
A	LEU156
A	HIS188
A	SER243
A	GLY15
A	SO4402
A	HOH517
A	HOH553
A	HOH561
A	HOH564
A	HOH567
A	HOH570
A	HOH571
A	HOH589
A	HOH599
A	GLN16
A	HOH600
A	HOH614
A	HOH631
A	HOH655
A	ILE17
A	ASP43
A	ILE44
A	VAL88
A	GLY89
A	GLY90

site_id	AC2
Number of Residues	10
Details	binding site for residue SO4 A 402

Chain	Residue
A	ASN132
A	ARG163
A	HIS188
A	GLY232
A	SER243
A	NAD401
A	HOH565
A	HOH611
A	HOH674
A	HOH679

site_id	AC3
Number of Residues	6
Details	binding site for residue SO4 A 403

Chain	Residue
A	ARG7
A	ILE38
A	HIS40
A	VAL70
A	HOH508
A	HOH520

site_id	AC4
Number of Residues	9
Details	binding site for residue GOL A 404

Chain	Residue
A	ILE299
A	VAL300
A	GLN301
A	HOH537
B	LYS100
B	ASP101
B	MET103
B	SER104
B	LEU326

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

Chain	Residue
A	GLN202
A	GLY206
A	GLU207
A	HOH514

site_id	AC6
Number of Residues	6
Details	binding site for residue PEO A 406

Chain	Residue
A	ARG163
A	GLY166
A	GLN167
A	ARG231
B	ILE59
B	ASP60

site_id	AC7
Number of Residues	7
Details	binding site for residue PEO A 407

Chain	Residue
A	ASP253
A	HOH598
A	HOH640
B	ARG27
B	ALA61
B	ALA62
B	HOH628

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

Chain	Residue
A	LYS142
A	GLU143
A	PRO146
A	HOH507
A	HOH601

site_id	AC9
Number of Residues	4
Details	binding site for residue FMT A 409

Chain	Residue
A	SER190
A	GLN230
A	HOH531
A	HOH597

site_id	AD1
Number of Residues	4
Details	binding site for residue TRS A 410

Chain	Residue
A	LYS215
A	ASP216
A	ASP217
A	ALA218

site_id	AD2
Number of Residues	7
Details	binding site for residue ETX A 411

Chain	Residue
A	GLN167
A	ARG231
A	HOH709
A	HOH760
B	SME56
B	ILE59
C	HOH792

site_id	AD3
Number of Residues	34
Details	binding site for residue NAD B 401

Chain	Residue
B	ILE17
B	ASP43
B	ILE44
B	VAL88
B	GLY89
B	GLY90
B	PHE91
B	PRO92
B	ILE109
B	GLN113
B	VAL130
B	ALA131
B	ASN132
B	LEU156
B	HIS188
B	SER242
B	SER243
B	SO4404
B	PEO411
B	HOH503
B	HOH512
B	HOH561
B	HOH562
B	HOH564
B	HOH585
B	HOH599
B	HOH604
B	HOH648
B	HOH670
B	HOH682
B	GLY12
B	ALA14
B	GLY15
B	GLN16

site_id	AD4
Number of Residues	8
Details	binding site for residue SO4 B 402

Chain	Residue
B	GLU98
B	ARG99
B	SER189
B	SER190
B	HOH592
B	HOH632
B	HOH654
B	HOH683

site_id	AD5
Number of Residues	9
Details	binding site for residue SO4 B 403

Chain	Residue
B	ARG7
B	ILE38
B	HIS40
B	VAL70
B	HOH502
B	HOH504
B	HOH571
B	HOH621
C	GLU170

site_id	AD6
Number of Residues	11
Details	binding site for residue SO4 B 404

Chain	Residue
B	ARG93
B	ARG99
B	ASN132
B	ARG163
B	HIS188
B	GLY232
B	SER243
B	NAD401
B	PEO411
B	EDO417
B	HOH549

site_id	AD7
Number of Residues	6
Details	binding site for residue GOL B 405

Chain	Residue
A	ILE59
B	GLN167
B	ARG231
B	HOH555
B	HOH581
B	HOH607

site_id	AD8
Number of Residues	5
Details	binding site for residue GOL B 406

Chain	Residue
B	ASN83
B	ASN124
B	LYS126
B	HOH541
B	HOH749

site_id	AD9
Number of Residues	8
Details	binding site for residue GOL B 407

Chain	Residue
A	ARG239
A	HOH683
B	ALA14
B	GLY15
B	GLN16
B	HOH511
B	HOH547
B	HOH630

site_id	AE1
Number of Residues	4
Details	binding site for residue PEO B 408

Chain	Residue
A	ASP60
B	ARG163
B	GLN167
B	ARG231

site_id	AE2
Number of Residues	4
Details	binding site for residue PEO B 409

Chain	Residue
B	LYS142
B	GLU143
B	PRO146
B	HOH536

site_id	AE3
Number of Residues	8
Details	binding site for residue PEO B 410

Chain	Residue
A	VAL176
A	HOH555
B	ILE59
B	PHE63
B	LEU66
B	HOH507
B	HOH530
B	HOH583

site_id	AE4
Number of Residues	5
Details	binding site for residue PEO B 411

Chain	Residue
B	GLY232
B	SER242
B	SER243
B	NAD401
B	SO4404

site_id	AE5
Number of Residues	5
Details	binding site for residue ACT B 412

Chain	Residue
B	ASP216
B	ASP217
B	ALA218
C	GLU318
C	LYS321

site_id	AE6
Number of Residues	2
Details	binding site for residue ACT B 413

Chain	Residue
B	PRO149
B	GLU150

site_id	AE7
Number of Residues	4
Details	binding site for residue ACT B 414

Chain	Residue
B	PRO281
B	SER282
B	HOH509
B	HOH663

site_id	AE8
Number of Residues	2
Details	binding site for residue FMT B 415

Chain	Residue
B	GLY206
B	GLU207

site_id	AE9
Number of Residues	2
Details	binding site for residue FMT B 416

Chain	Residue
B	LYS111
B	SER332

site_id	AF1
Number of Residues	10
Details	binding site for residue EDO B 417

Chain	Residue
B	ARG99
B	ASP160
B	ARG163
B	GLN192
B	VAL228
B	GLN229
B	ARG231
B	GLY232
B	SO4404
B	HOH613

site_id	AF2
Number of Residues	8
Details	binding site for residue EDO B 418

Chain	Residue
A	LYS180
A	LYS200
A	GLU207
B	ASP325
B	TYR328
B	SER329
B	HOH685
B	HOH734

site_id	AF3
Number of Residues	33
Details	binding site for residue NAD C 401

Chain	Residue
C	GLY12
C	GLY15
C	GLN16
C	ILE17
C	ASP43
C	ILE44
C	VAL88
C	GLY89
C	GLY90
C	PHE91
C	PRO92
C	ILE109
C	GLN113
C	VAL130
C	ALA131
C	ASN132
C	LEU156
C	HIS188
C	SER243
C	SO4402
C	PEO407
C	HOH520
C	HOH547
C	HOH554
C	HOH585
C	HOH593
C	HOH598
C	HOH601
C	HOH603
C	HOH604
C	HOH625
C	HOH658
C	HOH695

site_id	AF4
Number of Residues	10
Details	binding site for residue SO4 C 402

Chain	Residue
C	ASN132
C	ARG163
C	HIS188
C	GLY232
C	SER243
C	NAD401
C	HOH578
C	HOH620
C	HOH693
C	HOH741

site_id	AF5
Number of Residues	10
Details	binding site for residue SO4 C 403

Chain	Residue
A	GLU170
A	HOH652
B	HOH780
C	ARG7
C	ILE38
C	HIS40
C	VAL70
C	HOH501
C	HOH599
C	HOH629

site_id	AF6
Number of Residues	7
Details	binding site for residue SO4 C 404

Chain	Residue
A	ARG171
A	GLU223
A	HOH781
C	ALA122
C	PRO123
C	ASN124
C	HOH674

site_id	AF7
Number of Residues	7
Details	binding site for residue GOL C 405

Chain	Residue
C	SER277
C	TYR278
C	GLN301
C	GLY302
C	EDO412
C	HOH642
C	HOH725

site_id	AF8
Number of Residues	6
Details	binding site for residue PEO C 406

Chain	Residue
C	ILE59
C	ASP60
C	ARG163
C	GLY166
C	GLN167
C	ARG231

site_id	AF9
Number of Residues	5
Details	binding site for residue PEO C 407

Chain	Residue
C	ILE44
C	NAD401
C	HOH549
C	HOH552
C	HOH631

site_id	AG1
Number of Residues	7
Details	binding site for residue PEO C 408

Chain	Residue
C	ILE59
C	PHE63
C	LEU66
C	VAL176
C	HOH504
C	HOH590
C	HOH699

site_id	AG2
Number of Residues	7
Details	binding site for residue PEO C 409

Chain	Residue
C	GLN16
C	TYR19
C	ARG239
C	HOH521
C	HOH521
C	HOH662
C	HOH712

site_id	AG3
Number of Residues	4
Details	binding site for residue FMT C 410

Chain	Residue
C	SER190
C	GLN230
C	HOH519
C	HOH656

site_id	AG4
Number of Residues	7
Details	binding site for residue FMT C 411

Chain	Residue
C	VAL259
C	LEU260
C	GLY261
C	ARG293
C	ASN294
C	HOH508
C	HOH678

site_id	AG5
Number of Residues	6
Details	binding site for residue EDO C 412

Chain	Residue
C	TYR278
C	SER279
C	ARG310
C	GOL405
C	HOH507
C	HOH723

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
B	LEU156-ILE168
C	LEU156-ILE168

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P11708","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	27
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29194485","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5NUE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5NUF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Modified residue: {"description":"Methionine sulfoxide","evidences":[{"source":"PubMed","id":"29194485","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"19292762","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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