5NUF | pdb_00005nuf

Cytosolic Malate Dehydrogenase 1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5nufc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d5nufc2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d5nufb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d5nufb2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d5nufa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d5nufa2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8076630	3000039	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8076630	3000039	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LDH/MDH/AglA-like	8076630	3000039	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	SBP_bac_1	e5nufC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
B	SBP_bac_1	e5nufB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
A	Prenyltransf	e5nufA1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Prenyltransf	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02866	lactate/malate dehydrogenase, alpha/beta C-terminal domain (Ldh_1_C)	lactate/malate dehydrogenase, alpha/beta C-terminal domain	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the in ...	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.	Domain
A, B, C	PF00056	lactate/malate dehydrogenase, NAD binding domain (Ldh_1_N)	lactate/malate dehydrogenase, NAD binding domain	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the in ...	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Malate dehydrogenase 1, cytoplasmic	L-malate dehydrogenase (NAD+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors malate dehydrogenase activity catalytic activity RNA binding binding nucleic acid binding mRNA binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy response to stimulus response to metal ion response to chemical response to zinc ion oxoacid metabolic process malate metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy response to stimulus response to metal ion response to chemical response to zinc ion oxoacid metabolic process malate metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid metabolic process oxaloacetate metabolic process	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast extracellular region cytosol cell periphery membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast extracellular region cytosol cell periphery plasma membrane membrane cell-cell junction symplast anchoring junction cell junction plasmodesma apoplast plant-type vacuole vacuole nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B, C	IPR001252	Malate dehydrogenase, active site	Active Site
A, B, C	IPR001557	L-lactate/malate dehydrogenase	Family
A, B, C	IPR011274	Malate dehydrogenase, NAD-dependent, cytosolic	Family
A, B, C	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A, B, C	IPR010945	Malate dehydrogenase, type 2	Family
A, B, C	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.