3GVI | pdb_00003gvi

Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP

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)
F	d3gvif1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
F	d3gvif2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
E	d3gvie1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
E	d3gvie2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
D	d3gvid1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
D	d3gvid2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
C	d3gvic1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
C	d3gvic2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
B	d3gvib1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
B	d3gvib2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d3gvia1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d3gvia2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	LDH/MDH/AglA-like	8059726	3000039	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LDH/MDH/AglA-like	8059726	3000039	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8059726	3000039	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8059726	3000039	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8059726	3000039	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LDH/MDH/AglA-like	8059726	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)
F	RdRP_3	e3gviF2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
F		e3gviF3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (v294.1)
E	RdRP_3	e3gviE2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
E		e3gviE3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (v294.1)
D	RdRP_3	e3gviD2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
D		e3gviD3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (v294.1)
C	RdRP_3	e3gviC2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
C		e3gviC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (v294.1)
B	RdRP_3	e3gviB2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
B		e3gviB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (v294.1)
A	RdRP_3	e3gviA2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
A		e3gviA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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, D, E A, B, C, D, E, F	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	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	Malate dehydrogenase	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 L-lactate dehydrogenase (NAD+) activity L-2-hydroxycarboxylate dehydrogenase (NAD+) activity L-lactate dehydrogenase activity lactate dehydrogenase activity	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 oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process lactate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR011275	Malate dehydrogenase, type 3	Family
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.