Annotations: 5ESS

Crystal Structure of M. tuberculosis MenD bound to Mg2+ and covalent intermediate I (a ThDP and decarboxylated 2-oxoglutarate adduct)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	Lipoxygenase	e5essD2	A: alpha arrays	X: Alkaline phosphatase-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Lipoxygenase	ECOD (v295)
D	WD40	e5essD4	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: WD40	ECOD (v295)
C	Lipoxygenase	e5essC2	A: alpha arrays	X: Alkaline phosphatase-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Lipoxygenase	ECOD (v295)
C	WD40	e5essC4	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: WD40	ECOD (v295)
B	Lipoxygenase	e5essB2	A: alpha arrays	X: Alkaline phosphatase-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Lipoxygenase	ECOD (v295)
B	WD40	e5essB4	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: WD40	ECOD (v295)
A	Lipoxygenase	e5essA2	A: alpha arrays	X: Alkaline phosphatase-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Lipoxygenase	ECOD (v295)
A	WD40	e5essA4	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: WD40	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)
C	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02776	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N)	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity transketolase or transaldolase activity transferase activity catalytic activity vitamin binding thiamine pyrophosphate binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity transketolase or transaldolase activity transferase activity catalytic activity vitamin binding thiamine pyrophosphate binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	biosynthetic process small molecule biosynthetic process ketone metabolic process menaquinone metabolic process metabolic process cellular process small molecule metabolic process menaquinone biosynthetic process ketone biosynthetic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012001	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain	Domain
A, B, C, D	IPR004433	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase	Family
A, B, C, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily

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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.