6C1W | pdb_00006c1w

A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lactate racemase C-terminal domain-like	8091608	3002526	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lactate racemase N-terminal domain-like	8091607	3002525	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lactate racemase N-terminal domain-like	8091607	3002525	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lactate racemase C-terminal domain-like	8091608	3002526	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lactate racemase C-terminal domain-like	8091608	3002526	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lactate racemase N-terminal domain-like	8091607	3002525	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)
A	DUF2088	e6c1wA2	A: a/b three-layered sandwiches	X: Lactate racemase N-terminal domain (From Topology)	H: Lactate racemase N-terminal domain (From Topology)	T: Lactate racemase N-terminal domain	F: DUF2088	ECOD (1.6)
A	LarA	e6c1wA1	A: a/b three-layered sandwiches	X: Lactate racemase C-terminal domain (From Topology)	H: Lactate racemase C-terminal domain (From Topology)	T: Lactate racemase C-terminal domain	F: LarA	ECOD (1.6)
B	DUF2088	e6c1wB1	A: a/b three-layered sandwiches	X: Lactate racemase N-terminal domain (From Topology)	H: Lactate racemase N-terminal domain (From Topology)	T: Lactate racemase N-terminal domain	F: DUF2088	ECOD (1.6)
B	LarA	e6c1wB2	A: a/b three-layered sandwiches	X: Lactate racemase C-terminal domain (From Topology)	H: Lactate racemase C-terminal domain (From Topology)	T: Lactate racemase C-terminal domain	F: LarA	ECOD (1.6)
C	DUF2088	e6c1wC2	A: a/b three-layered sandwiches	X: Lactate racemase N-terminal domain (From Topology)	H: Lactate racemase N-terminal domain (From Topology)	T: Lactate racemase N-terminal domain	F: DUF2088	ECOD (1.6)
C	LarA	e6c1wC1	A: a/b three-layered sandwiches	X: Lactate racemase C-terminal domain (From Topology)	H: Lactate racemase C-terminal domain (From Topology)	T: Lactate racemase C-terminal domain	F: LarA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.226.30	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
A	3.40.50.11440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	LarA, N-terminal domain	CATH (4.3.0)
B	3.90.226.30	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
B	3.40.50.11440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	LarA, N-terminal domain	CATH (4.3.0)
C	3.90.226.30	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
C	3.40.50.11440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	LarA, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09861	Lactate racemase N-terminal domain (Lar_N)	Lactate racemase N-terminal domain	This is the N-terminal domain found in Lactate racemase enzymes EC:5.1.2.1. LarA is a nickel-dependent lactate racemase from the larA-E operon of Lactobacillus plantarum, whereas LarB, LarC and LarE are accessory proteins required for the incorporati ...	This is the N-terminal domain found in Lactate racemase enzymes EC:5.1.2.1. LarA is a nickel-dependent lactate racemase from the larA-E operon of Lactobacillus plantarum, whereas LarB, LarC and LarE are accessory proteins required for the incorporation of Ni in the lactate racemase apoprotein. LarA contains 18 beta-strands and 16 alpha-helices arranged in a novel fold composed of two domains of similar size. This entry represents the N-terminal domain of LarA and related proteins [1].	Domain
A, B, C	PF21113	Lactate racemase C-terminal domain (LarA_C)	Lactate racemase C-terminal domain	This entry represents the C-terminal domain of the nickel-dependent lactate racemase enzyme (LarA) [1]. LarA is part of a superfamily containing many different enzymes [4]. These include malate racemases, phenyllactate racemase, one alpha-hydroxyglut ...	This entry represents the C-terminal domain of the nickel-dependent lactate racemase enzyme (LarA) [1]. LarA is part of a superfamily containing many different enzymes [4]. These include malate racemases, phenyllactate racemase, one alpha-hydroxyglutarate racemase, D-gluconate 2-epimerase, a short-chain aliphatic alpha-hydroxyacid racemase [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Lactate racemase	racemase and epimerase activity, acting on hydroxy acids and derivatives isomerase activity racemase and epimerase activity lactate racemase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR048520	Lactate racemase, C-terminal domain	Domain
A, B, C	IPR043166	LarA-like, C-terminal domain	Homologous Superfamily
A, B, C	IPR048068	LarA-like	Family
A, B, C	IPR018657	LarA-like, N-terminal	Domain
A, B, C	IPR047926	Nickel-dependent lactate racemase LarA	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.