6J9U | pdb_00006j9u

Complex structure of Lactobacillus casei lactate dehydrogenase penta mutant with pyruvate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d6j9ua1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
A	d6j9ua2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
B	d6j9ub1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
B	d6j9ub2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
C	d6j9uc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
C	d6j9uc2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
D	d6j9ud1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
D	d6j9ud2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
E	d6j9ue1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
E	d6j9ue2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
F	d6j9uf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)
F	d6j9uf2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	automated matches	(Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 ) [TaxId: 1423732 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	LDH/MDH/AglA-like	8057324	3000039	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8057324	3000039	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8057324	3000039	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8057324	3000039	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LDH/MDH/AglA-like	8057324	3000039	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LDH/MDH/AglA-like	8057324	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	bCoV_S1_N	e6j9uA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: bCoV_S1_N	ECOD (v294.1)
B	bCoV_S1_N	e6j9uB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: bCoV_S1_N	ECOD (v294.1)
C	bCoV_S1_N	e6j9uC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: bCoV_S1_N	ECOD (v294.1)
D	bCoV_S1_N	e6j9uD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: bCoV_S1_N	ECOD (v294.1)
E	bCoV_S1_N	e6j9uE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: bCoV_S1_N	ECOD (v294.1)
F	bCoV_S1_N	e6j9uF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: bCoV_S1_N	ECOD (v294.1)

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	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)
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)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	L-lactate dehydrogenase	L-lactate dehydrogenase (NAD+) activity L-2-hydroxycarboxylate dehydrogenase (NAD+) activity oxidoreductase activity L-lactate dehydrogenase 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 catalytic activity	ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process purine ribonucleoside diphosphate catabolic process lactate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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

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.