5EJM: ThDP-Mn2+ complex of R413A variant of EcMenD soaked with 2-ketoglutarate for 35 min

PDB ID: 5EJMDownload
MMDB ID: 144501
PDB Deposition Date: 2015/11/2
Updated in MMDB: 2018/11
Experimental Method:
x-ray diffraction
Resolution: 1.72  Å
Source Organism:
Similar Structures:
Biological Unit for 5EJM: dimeric; determined by author and by software (PISA)
Molecular Components in 5EJM
Label Count Molecule
Proteins (2 molecules)
2
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate Synthase
(Gene symbol: menD)
Molecule annotation
Chemicals and Non-standard biopolymers (8 molecules)
1
2
(4~{R})-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(4~{R})-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
2
2
MANGANESE (II) IONMANGANESE (II) ION
3
2
GLYCEROLGLYCEROL
4
2
1,2-ETHANEDIOL1,2-ETHANEDIOL
* 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