5ESS

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

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, C, D	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	polymer	574	60068.9	4	UniProt (P9WK11) Pfam (PF02776) In PDB	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	SEPHCHC synthase,Menaquinone biosynthesis protein MenD
2	A, C, D	MAGNESIUM ION	non-polymer		24.3	3	Chemie (MG)
3	A, B, C, D	FORMIC ACID	non-polymer		46.0	10	Chemie (FMT)
4	A	DIPHOSPHATE	non-polymer		173.9	1	Chemie (DPO)
5	B	GLYCEROL	non-polymer		92.1	1	Chemie (GOL)
6	C, D	4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid	non-polymer		526.4	2	Chemie (TOG)
7	D	ACETATE ION	non-polymer		59.0	3	Chemie (ACT)
8		water	water		18.0	586	Chemie (HOH)

Sequence modifications

A, B, C, D: 1 - 554 (UniProt: P9WK11)

PDB	External Database	Details
Met -19	-	initiating methionine
Gly -18	-	expression tag
Ser -17	-	expression tag
Ser -16	-	expression tag
His -15	-	expression tag
His -14	-	expression tag
His -13	-	expression tag
His -12	-	expression tag
His -11	-	expression tag
His -10	-	expression tag
Ser -9	-	expression tag
Ser -8	-	expression tag
Gly -7	-	expression tag
Leu -6	-	expression tag
Val -5	-	expression tag
Pro -4	-	expression tag
Arg -3	-	expression tag
Gly -2	-	expression tag
Ser -1	-	expression tag
His 0	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	240275.8
Non-Polymers*	Number of molecules	20
	Total formula weight	2029.1
All*	Total formula weight	242304.9

*Water molecules are not included.