5ES3

Co-crystal structure of LDH liganded with oxamate

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5es3a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d5es3a2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth C]	d5es3c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth C]	d5es3c2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth E]	d5es3e1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth E]	d5es3e2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D [auth F]	d5es3f1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D [auth F]	d5es3f2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E [auth D]	d5es3d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E [auth D]	d5es3d2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F [auth H]	d5es3h1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F [auth H]	d5es3h2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G [auth B]	d5es3b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G [auth B]	d5es3b2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
H [auth G]	d5es3g1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
H [auth G]	d5es3g2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	LDH/MDH-like	8059703	4000045	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2 (2022-06-29)
B [auth C]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2B (2022-06-29)
F [auth H]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	3000039	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059704	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)
A	Ldh_1_C_13	e5es3A3	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
A	Ldh_1_N	e5es3A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
B [auth C]	Ldh_1_C_13	e5es3C2	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
B [auth C]	Ldh_1_N	e5es3C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
C [auth E]	Ldh_1_C_13	e5es3E1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
C [auth E]	Ldh_1_N	e5es3E2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
D [auth F]	Ldh_1_C_13	e5es3F3	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
D [auth F]	Ldh_1_N	e5es3F2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
E [auth D]	Ldh_1_C_13	e5es3D3	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
E [auth D]	Ldh_1_N	e5es3D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
F [auth H]	Ldh_1_C_13	e5es3H2	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
F [auth H]	Ldh_1_N	e5es3H1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
G [auth B]	Ldh_1_C_13	e5es3B3	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
G [auth B]	Ldh_1_N	e5es3B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
H [auth G]	Ldh_1_C_13	e5es3G2	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_13	ECOD (1.6)
H [auth G]	Ldh_1_N	e5es3G1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B [auth C]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth C]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
C [auth E]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth E]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
D [auth F]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth F]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
E [auth D]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E [auth D]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
F [auth H]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F [auth H]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
G [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G [auth B]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
H [auth G]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H [auth G]	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 [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	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 [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	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 [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	L-lactate dehydrogenase A chain	protein binding binding kinase binding enzyme binding 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 lactate dehydrogenase activity L-lactate dehydrogenase activity catalytic activity NAD binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding protein binding binding kinase binding enzyme binding 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 lactate dehydrogenase activity L-lactate dehydrogenase activity catalytic activity NAD binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding identical protein binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development response to stimulus response to chemical response to xenobiotic stimulus response to organic substance response to hormone developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development response to stimulus response to chemical response to xenobiotic stimulus response to organic substance response to hormone response to endogenous stimulus response to estrogen pyruvate metabolic process organic substance metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process organic hydroxy compound metabolic process lactate metabolic process muscle structure development skeletal muscle organ development skeletal muscle tissue development muscle tissue development muscle organ development tissue development response to extracellular stimulus cellular response to stimulus cellular response to extracellular stimulus response to external stimulus cell communication cellular response to external stimulus NAD metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process heterocycle metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process nitrogen compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process organic cyclic compound metabolic process organophosphate metabolic process cellular aromatic compound metabolic process response to hexose response to monosaccharide response to carbohydrate response to glucose response to oxygen-containing compound response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus monosaccharide metabolic process catabolic process glucose catabolic process to lactate via pyruvate energy derivation by oxidation of organic compounds carbohydrate catabolic process fermentation glycolytic fermentation carbohydrate metabolic process hexose catabolic process hexose metabolic process generation of precursor metabolites and energy glucose catabolic process glucose catabolic process to lactate monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process response to organonitrogen compound response to organophosphorus response to nitrogen compound response to purine-containing compound response to cAMP response to organic cyclic compound response to nutrient levels response to nutrient organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process pyruvate catabolic process response to hydrogen peroxide response to oxidative stress response to reactive oxygen species response to inorganic substance	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol cell projection sperm fibrous sheath cilium 9+2 motile cilium sperm flagellum membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol cell projection sperm fibrous sheath cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection protein-containing complex catalytic complex oxidoreductase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR011304	L-lactate dehydrogenase	Family
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR018177	L-lactate dehydrogenase, active site	Active Site
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR001557	L-lactate/malate dehydrogenase	Family
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A, B [auth C], C [auth E], D [auth F], E [auth D], A, B [auth C], C [auth E], D [auth F], E [auth D], F [auth H], G [auth B], H [auth G]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.