3FI9 | pdb_00003fi9

Crystal structure of malate dehydrogenase from Porphyromonas gingivalis

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)
B	d3fi9b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Porphyromonas gingivalis ATCC 33277 ) [TaxId: 431947 ],	SCOPe (2.08)
B	d3fi9b2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Porphyromonas gingivalis ATCC 33277 ) [TaxId: 431947 ],	SCOPe (2.08)
B	d3fi9b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Porphyromonas gingivalis ATCC 33277 ) [TaxId: 431947 ],	SCOPe (2.08)
A	d3fi9a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Porphyromonas gingivalis ATCC 33277 ) [TaxId: 431947 ],	SCOPe (2.08)
A	d3fi9a2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Porphyromonas gingivalis ATCC 33277 ) [TaxId: 431947 ],	SCOPe (2.08)
A	d3fi9a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Porphyromonas gingivalis ATCC 33277 ) [TaxId: 431947 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8059758	3000039	SCOP2B (2022-06-29)
A	SCOP2 Family	LDH/MDH-like	8059757	4000045	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LDH/MDH/AglA-like	8059758	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)
B	Ldh_1_C_10	e3fi9B1	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_10	ECOD (1.6)
B	Ldh_1_N	e3fi9B2	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_10	e3fi9A3	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_10	ECOD (1.6)
A	Ldh_1_N	e3fi9A2	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)
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	Malate 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 catalytic activity malate dehydrogenase activity	oxoacid metabolic process malate metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A, B	IPR010945	Malate dehydrogenase, type 2	Family
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain
A, B	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.