Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4WLV

Crystal structure of NAD bound MDH2

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	27
Details	binding site for residue NAD A 401

Chain	Residue
A	SER33
A	GLY101
A	VAL102
A	PRO103
A	LEU113
A	ASN117
A	ILE120
A	ILE140
A	ALA141
A	ASN142
A	VAL169
A	GLY34
A	HIS200
A	ALA247
A	MET251
A	PO4402
A	PO4403
A	HOH510
A	HOH515
A	HOH520
A	GLY35
A	ILE36
A	TYR56
A	ASP57
A	ILE58
A	PRO99
A	ALA100

site_id	AC2
Number of Residues	7
Details	binding site for residue PO4 A 402

Chain	Residue
A	PRO103
A	ARG104
A	ARG110
A	ASN142
A	SER246
A	NAD401
A	PO4403

site_id	AC3
Number of Residues	8
Details	binding site for residue PO4 A 403

Chain	Residue
A	ARG104
A	ARG110
A	ASN142
A	ARG176
A	HIS200
A	GLY234
A	NAD401
A	PO4402

site_id	AC4
Number of Residues	24
Details	binding site for residue NAD B 401

Chain	Residue
B	SER33
B	GLY34
B	GLY35
B	ILE36
B	TYR56
B	ASP57
B	ILE58
B	PRO99
B	ALA100
B	GLY101
B	VAL102
B	PRO103
B	ASN117
B	ILE120
B	ILE140
B	ASN142
B	VAL169
B	HIS200
B	ALA247
B	THR248
B	MET251
B	PO4402
B	PO4403
B	HOH511

site_id	AC5
Number of Residues	7
Details	binding site for residue PO4 B 402

Chain	Residue
B	PRO103
B	ARG104
B	LEU113
B	ASN142
B	SER246
B	NAD401
B	PO4403

site_id	AC6
Number of Residues	8
Details	binding site for residue PO4 B 403

Chain	Residue
B	ARG104
B	ARG110
B	ASN142
B	ARG176
B	HIS200
B	GLY234
B	NAD401
B	PO4402

site_id	AC7
Number of Residues	25
Details	binding site for residue NAD C 401

Chain	Residue
C	THR248
C	MET251
C	PO4402
C	PO4403
C	HOH505
C	HOH507
C	HOH508
C	SER33
C	GLY34
C	GLY35
C	ILE36
C	TYR56
C	ASP57
C	ILE58
C	PRO99
C	ALA100
C	GLY101
C	VAL102
C	PRO103
C	ASN117
C	ILE140
C	ASN142
C	VAL169
C	HIS200
C	ALA247

site_id	AC8
Number of Residues	7
Details	binding site for residue PO4 C 402

Chain	Residue
C	PRO103
C	ARG104
C	LEU113
C	ASN142
C	SER246
C	NAD401
C	PO4403

site_id	AC9
Number of Residues	8
Details	binding site for residue PO4 C 403

Chain	Residue
C	ARG104
C	ARG110
C	ASN142
C	ARG176
C	HIS200
C	GLY234
C	NAD401
C	PO4402

site_id	AD1
Number of Residues	24
Details	binding site for residue NAD D 401

Chain	Residue
D	SER33
D	GLY34
D	GLY35
D	ILE36
D	TYR56
D	ASP57
D	ILE58
D	PRO99
D	ALA100
D	GLY101
D	VAL102
D	PRO103
D	ASN117
D	ILE120
D	ILE140
D	ASN142
D	VAL169
D	HIS200
D	ALA247
D	THR248
D	MET251
D	PO4402
D	PO4403
D	HOH504

site_id	AD2
Number of Residues	8
Details	binding site for residue PO4 D 402

Chain	Residue
D	ARG104
D	ARG110
D	ASN142
D	ARG176
D	HIS200
D	GLY234
D	NAD401
D	PO4403

site_id	AD3
Number of Residues	6
Details	binding site for residue PO4 D 403

Chain	Residue
D	PRO103
D	ARG104
D	ASN142
D	SER246
D	NAD401
D	PO4402

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	VAL169-VAL181

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

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