3PQD

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

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	d3pqda1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d3pqda2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d3pqdb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d3pqdb2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d3pqdc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d3pqdc2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d3pqdd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d3pqdd2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d3pqde1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d3pqde2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d3pqdf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d3pqdf2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d3pqdg1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d3pqdg2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d3pqdh1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d3pqdh2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	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	8059686	3000039	SCOP2B (2022-06-29)
B	SCOP2 Family	LDH/MDH-like	8059685	4000045	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	LDH/MDH/AglA-like	8059686	3000039	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8059686	3000039	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8059686	3000039	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LDH/MDH/AglA-like	8059686	3000039	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LDH/MDH/AglA-like	8059686	3000039	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LDH/MDH/AglA-like	8059686	3000039	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	LDH/MDH/AglA-like	8059686	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_2	e3pqdA3	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_2	ECOD (1.6)
A	Ldh_1_N	e3pqdA2	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	Ldh_1_C_2	e3pqdB3	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_2	ECOD (1.6)
B	Ldh_1_N	e3pqdB2	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	Ldh_1_C_2	e3pqdC2	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_2	ECOD (1.6)
C	Ldh_1_N	e3pqdC3	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	Ldh_1_C_2	e3pqdD2	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_2	ECOD (1.6)
D	Ldh_1_N	e3pqdD3	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	Ldh_1_C_2	e3pqdE3	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_2	ECOD (1.6)
E	Ldh_1_N	e3pqdE2	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	Ldh_1_C_2	e3pqdF3	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_2	ECOD (1.6)
F	Ldh_1_N	e3pqdF2	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	Ldh_1_C_2	e3pqdG2	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_2	ECOD (1.6)
G	Ldh_1_N	e3pqdG3	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	Ldh_1_C_2	e3pqdH2	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_2	ECOD (1.6)
H	Ldh_1_N	e3pqdH3	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	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)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	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, D, E A, B, C, D, E, F, G, H	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, D, E A, B, C, D, E, F, G, H	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, D, E A, B, C, D, E, F, G, H	L-lactate dehydrogenase	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	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 ribonucleotide catabolic process pyridine nucleotide catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process 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 ribonucleotide catabolic process pyridine nucleotide catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process nicotinamide nucleotide metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process catabolic process ATP metabolic process 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 ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process ADP catabolic process generation of precursor metabolites and energy organic cyclic compound catabolic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process organic substance catabolic process purine ribonucleoside diphosphate catabolic process organic hydroxy compound metabolic process lactate metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

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.