5ESS: Crystal Structure of M. tuberculosis MenD bound to Mg2+ and covalent intermediate I (a ThDP and decarboxylated 2-oxoglutarate adduct)

PDB ID: 5ESSDownload
MMDB ID: 140239
PDB Deposition Date: 2015/11/17
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
Similar Structures:
Biological Unit for 5ESS: tetrameric; determined by author and by software (PISA)
Molecular Components in 5ESS
Label Count Molecule
Proteins (4 molecules)
4
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate Synthase
(Gene symbol: menD)
Molecule annotation
Chemicals and Non-standard biopolymers (20 molecules)
1
3
MAGNESIUM IONMAGNESIUM ION
2
10
FORMIC ACIDFORMIC ACID
3
1
DIPHOSPHATEDIPHOSPHATE
4
1
GLYCEROLGLYCEROL
5
2
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 acid4-[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
6
3
ACETATE IONACETATE ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303