4PLY | pdb_00004ply

Crystal structure of ancestral apicomplexan malate dehydrogenase with malate.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	3000039	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	LDH/MDH/AglA-like	8059724	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)
H	YajR_YAM	e4plyH1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
H	EPSP_synthase	e4plyH2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
G	YajR_YAM	e4plyG1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
G	EPSP_synthase	e4plyG2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
F [auth E]	YajR_YAM	e4plyE1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
F [auth E]	EPSP_synthase	e4plyE2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
E [auth F]	YajR_YAM	e4plyF1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
E [auth F]	EPSP_synthase	e4plyF2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
D	YajR_YAM	e4plyD1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
D	EPSP_synthase	e4plyD2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
C	YajR_YAM	e4plyC1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
C	EPSP_synthase	e4plyC2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
B [auth A]	YajR_YAM	e4plyA1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
B [auth A]	EPSP_synthase	e4plyA2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)
A [auth B]	YajR_YAM	e4plyB1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
A [auth B]	EPSP_synthase	e4plyB2	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
F [auth E]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F [auth E]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
E [auth F]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E [auth F]	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 [auth A]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth A]	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
A [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A [auth B]	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 [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	malate 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 binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process lactate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	IPR011275	Malate dehydrogenase, type 3	Family
A [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain
A [auth B], B [auth A], C, D, E [auth F], A [auth B], B [auth A], C, D, E [auth F], F [auth E], G, H	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.