Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2DFD

Crystal Structure of Human Malate Dehydrogenase Type 2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003723	molecular_function	RNA binding
A	0003824	molecular_function	catalytic activity
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0006094	biological_process	gluconeogenesis
A	0006099	biological_process	tricarboxylic acid cycle
A	0006108	biological_process	malate metabolic process
A	0009060	biological_process	aerobic respiration
A	0016020	cellular_component	membrane
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	0042802	molecular_function	identical protein binding
A	0043490	biological_process	malate-aspartate shuttle
A	0046554	molecular_function	L-malate dehydrogenase (NADP+) activity
A	0070062	cellular_component	extracellular exosome
B	0003723	molecular_function	RNA binding
B	0003824	molecular_function	catalytic activity
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0006094	biological_process	gluconeogenesis
B	0006099	biological_process	tricarboxylic acid cycle
B	0006108	biological_process	malate metabolic process
B	0009060	biological_process	aerobic respiration
B	0016020	cellular_component	membrane
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	0042802	molecular_function	identical protein binding
B	0043490	biological_process	malate-aspartate shuttle
B	0046554	molecular_function	L-malate dehydrogenase (NADP+) activity
B	0070062	cellular_component	extracellular exosome
C	0003723	molecular_function	RNA binding
C	0003824	molecular_function	catalytic activity
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0006094	biological_process	gluconeogenesis
C	0006099	biological_process	tricarboxylic acid cycle
C	0006108	biological_process	malate metabolic process
C	0009060	biological_process	aerobic respiration
C	0016020	cellular_component	membrane
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	0042802	molecular_function	identical protein binding
C	0043490	biological_process	malate-aspartate shuttle
C	0046554	molecular_function	L-malate dehydrogenase (NADP+) activity
C	0070062	cellular_component	extracellular exosome
D	0003723	molecular_function	RNA binding
D	0003824	molecular_function	catalytic activity
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0006094	biological_process	gluconeogenesis
D	0006099	biological_process	tricarboxylic acid cycle
D	0006108	biological_process	malate metabolic process
D	0009060	biological_process	aerobic respiration
D	0016020	cellular_component	membrane
D	0016491	molecular_function	oxidoreductase activity
D	0016615	molecular_function	malate dehydrogenase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0019752	biological_process	carboxylic acid metabolic process
D	0030060	molecular_function	L-malate dehydrogenase (NAD+) activity
D	0042802	molecular_function	identical protein binding
D	0043490	biological_process	malate-aspartate shuttle
D	0046554	molecular_function	L-malate dehydrogenase (NADP+) activity
D	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE LMR D 3101

Chain	Residue
D	ARG86
D	ARG92
D	ASN124
D	ARG158
D	HIS182
D	GLY216
D	NAD3004
D	HOH3399
D	HOH3400

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE LMR B 3102

Chain	Residue
B	ARG86
B	ARG92
B	ASN124
B	ARG158
B	HIS182
B	GLY216
B	NAD3001
B	HOH3405
B	HOH3528

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LMR C 3103

Chain	Residue
C	ARG86
C	ARG92
C	ASN124
C	ARG158
C	HIS182
C	GLY216
C	ALA229
C	NAD3002
C	HOH3509
C	HOH3729

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LMR A 3104

Chain	Residue
A	ARG86
A	ARG92
A	ASN124
A	ARG158
A	HIS182
A	GLY216
A	ALA229
A	NAD3003
A	HOH3337
A	HOH3341

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL C 3201

Chain	Residue
C	ARG92
C	HOH3553

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL D 3202

Chain	Residue
D	ARG92
D	HOH3318

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL A 3203

Chain	Residue
A	ARG92

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL C 3204

Chain	Residue
C	GLN263
C	HOH3597

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL A 3205

Chain	Residue
A	ASN146

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 3206

Chain	Residue
B	VAL198
B	PHE200
B	HOH3533

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL D 3207

Chain	Residue
D	VAL198
D	HOH3416

site_id	BC3
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD B 3001

Chain	Residue
B	SER15
B	GLY16
B	GLY17
B	ILE18
B	TYR38
B	ASP39
B	ILE40
B	PRO81
B	ALA82
B	GLY83
B	VAL84
B	PRO85
B	ASN99
B	ILE102
B	ILE122
B	ASN124
B	VAL151
B	HIS182
B	ALA229
B	THR230
B	MET233
B	LMR3102
B	HOH3404
B	HOH3405
B	HOH3415
B	HOH3420
B	HOH3429
B	HOH3452
B	HOH3476
B	HOH3497
B	HOH3501
B	HOH3519
B	HOH3527

site_id	BC4
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAD C 3002

Chain	Residue
C	ILE102
C	ILE122
C	ASN124
C	VAL126
C	VAL151
C	HIS182
C	ALA229
C	THR230
C	MET233
C	LMR3103
C	HOH3509
C	HOH3520
C	HOH3526
C	HOH3540
C	HOH3557
C	HOH3626
C	HOH3636
C	HOH3646
C	HOH3691
C	HOH3730
C	GLY13
C	SER15
C	GLY16
C	GLY17
C	ILE18
C	TYR38
C	ASP39
C	ILE40
C	PRO81
C	ALA82
C	GLY83
C	VAL84
C	PRO85
C	LEU95
C	ASN99

site_id	BC5
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD A 3003

Chain	Residue
A	SER15
A	GLY16
A	GLY17
A	ILE18
A	TYR38
A	ASP39
A	ILE40
A	PRO81
A	ALA82
A	GLY83
A	VAL84
A	PRO85
A	ASN99
A	ILE102
A	ILE122
A	ASN124
A	VAL126
A	VAL151
A	HIS182
A	ALA229
A	THR230
A	MET233
A	LMR3104
A	HOH3304
A	HOH3305
A	HOH3337
A	HOH3344
A	HOH3347
A	HOH3379
A	HOH3389
A	HOH3427
A	HOH3476
A	HOH3478

site_id	BC6
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAD D 3004

Chain	Residue
D	SER15
D	GLY16
D	GLY17
D	ILE18
D	TYR38
D	ASP39
D	ILE40
D	PRO81
D	ALA82
D	GLY83
D	VAL84
D	PRO85
D	LEU95
D	ASN99
D	ILE102
D	ILE122
D	ASN124
D	VAL126
D	VAL151
D	HIS182
D	ALA229
D	THR230
D	MET233
D	LMR3101
D	HOH3220
D	HOH3224
D	HOH3236
D	HOH3237
D	HOH3251
D	HOH3313
D	HOH3335
D	HOH3341
D	HOH3361
D	HOH3393
D	HOH3399

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE HIS A 3301

Chain	Residue
A	ASN160
A	PRO171
A	ALA172
A	VAL174
A	ASN175
A	ARG239
A	ALA3302
B	GLU54
B	HOH3434

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ALA A 3302

Chain	Residue
A	ARG239
A	SER243
A	HIS3301
A	HOH3359

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE HIS B 3401

Chain	Residue
A	GLU54
B	ASN160
B	PRO171
B	ALA172
B	VAL174
B	ASN175
B	ARG239

site_id	CC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE HIS C 3501

Chain	Residue
C	ASN160
C	PRO171
C	ALA172
C	VAL174
C	ASN175
C	ARG239
D	GLU54

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	VAL151-VAL163

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P00346","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	44
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human malate dehydrogenase type 2.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10004","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human malate dehydrogenase type 2.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	36
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P08249","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P08249","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q32LG3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	8
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q32LG3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P04636","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
A	ASP155
A	HIS182

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
B	ASP155
B	HIS182

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
C	ASP155
C	HIS182

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
D	ASP155
D	HIS182

site_id	CSA5
Number of Residues	3
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
A	ASP155
A	HIS182
A	ARG158

site_id	CSA6
Number of Residues	3
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
B	ASP155
B	HIS182
B	ARG158

site_id	CSA7
Number of Residues	3
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
C	ASP155
C	HIS182
C	ARG158

site_id	CSA8
Number of Residues	3
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
D	ASP155
D	HIS182
D	ARG158

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