4BGV | pdb_00004bgv

1.8 A resolution structure of the malate dehydrogenase from Picrophilus torridus in its apo form

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)
D	d4bgvd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
D	d4bgvd2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
C	d4bgvc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
C	d4bgvc2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
B	d4bgvb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
B	d4bgvb2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
A	d4bgva1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)
A	d4bgva2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Picrophilus oshimae ) [TaxId: 46632 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8059740	3000039	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8059740	3000039	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8059740	3000039	SCOP2B (2022-06-29)
A	SCOP2 Family	LDH/MDH-like	8059739	4000045	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LDH/MDH/AglA-like	8059740	3000039	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Ldh_1_C_7	e4bgvD2	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_7	ECOD (1.6)
D	Ldh_1_N	e4bgvD1	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_7	e4bgvC2	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_7	ECOD (1.6)
C	Ldh_1_N	e4bgvC1	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_7	e4bgvB2	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_7	ECOD (1.6)
B	Ldh_1_N	e4bgvB1	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)
A	Ldh_1_C_7	e4bgvA2	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_7	ECOD (1.6)
A	Ldh_1_N	e4bgvA1	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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	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	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR011275	Malate dehydrogenase, type 3	Family
A, B, C, D	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B, C, D	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain
A, B, C, D	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.