5VIT

Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CoA_trans	e5vitA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: CoA_trans	ECOD (1.6)
A	UNK_F_TYPE	e5vitA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: UNK_F_TYPE	ECOD (1.6)
E [auth P]	CoA_trans	e5vitP2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: CoA_trans	ECOD (1.6)
E [auth P]	UNK_F_TYPE	e5vitP1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: UNK_F_TYPE	ECOD (1.6)
I	CoA_trans	e5vitI2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: CoA_trans	ECOD (1.6)
I	UNK_F_TYPE	e5vitI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: UNK_F_TYPE	ECOD (1.6)
M [auth V]	CoA_trans	e5vitV2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: CoA_trans	ECOD (1.6)
M [auth V]	UNK_F_TYPE	e5vitV1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: UNK_F_TYPE	ECOD (1.6)
B [auth C]	UNK_F_TYPE	e5vitC1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: UNK_F_TYPE	ECOD (1.6)
F [auth R]	UNK_F_TYPE	e5vitR1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: UNK_F_TYPE	ECOD (1.6)
J [auth K]	UNK_F_TYPE	e5vitK1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: UNK_F_TYPE	ECOD (1.6)
N [auth X]	UNK_F_TYPE	e5vitX1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: UNK_F_TYPE	ECOD (1.6)
C [auth D]	Carboxyl_trans_N	e5vitD1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_N	ECOD (1.6)
G [auth S]	Carboxyl_trans_N	e5vitS1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_N	ECOD (1.6)
K [auth L]	Carboxyl_trans_N	e5vitL1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_N	ECOD (1.6)
O [auth Y]	Carboxyl_trans_N	e5vitY1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_N	ECOD (1.6)
D [auth E]	ACCA	e5vitE1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: ACCA	ECOD (1.6)
H [auth T]	ACCA	e5vitT1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: ACCA	ECOD (1.6)
L [auth M]	ACCA	e5vitM1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: ACCA	ECOD (1.6)
P [auth Z]	ACCA	e5vitZ1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: ACCA	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth P], I, M [auth V]	PF16957	Malonate decarboxylase, alpha subunit, transporter (Mal_decarbox_Al)	Malonate decarboxylase, alpha subunit, transporter	-	Family
B [auth C], F [auth R], J [auth K], N [auth X]	PF06857	Malonate decarboxylase delta subunit (MdcD) (ACP)	Malonate decarboxylase delta subunit (MdcD)	-	Family
C [auth D], G [auth S], K [auth L], O [auth Y]	PF01039	Carboxyl transferase domain (Carboxyl_trans)	Carboxyl transferase domain	-	Family
D [auth E], H [auth T], L [auth M], P [auth Z]	PF06833	Malonate decarboxylase gamma subunit (MdcE) (MdcE)	Malonate decarboxylase gamma subunit (MdcE)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth P], I, M [auth V]	MdcA	transferase activity catalytic activity	-	-
B [auth C], F [auth R], J [auth K], N [auth X]	MdcC	phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity
C [auth D], G [auth S], K [auth L], O [auth Y]	MdcD	carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process	-
D [auth E], H [auth T], L [auth M], P [auth Z]	MdcE	-	carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth P], I, M [auth V]	IPR005777	Acetyl-S-ACP:malonate ACP transferase	Family
A, E [auth P], I, M [auth V]	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
B [auth C], F [auth R], J [auth K], N [auth X]	IPR023439	Malonate decarboxylase/citrate lyase acyl carrier protein	Family
B [auth C], F [auth R], J [auth K], N [auth X]	IPR009662	Malonate decarboxylase delta subunit	Family
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR017556	Biotin-independent malonate decarboxylase, beta subunit	Family
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain
D [auth E], H [auth T], L [auth M], P [auth Z]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
D [auth E], H [auth T], L [auth M], P [auth Z]	IPR009648	Biotin-dependent malonate decarboxylase, gamma subunit	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.

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5VIT

Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage