Crystal structure of M. tuberculosis mend bound to MG2+ and covalent intermediate II (a thdp + de-carboxylated 2-oxoglutarate + isochorismate adduct)

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).

Ligands and binding sites

• TOI · (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl (phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxid anyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic acid · ligand · 2 copies · chains B, C, A, D
• MG · Magnesium ion · metal · 3 copies · chains A, C, D
• FMT · Formic acid · additive · 2 copies · chains A, B
• BME · Beta-mercaptoethanol · additive · 2 copies · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–D · 3331 Ų buried · 50 hydrogen bonds · protein-protein
• B–C · 3246 Ų buried · 45 hydrogen bonds · protein-protein
• A–C · 1541 Ų buried · 44 hydrogen bonds · protein-protein
• B–D · 1525 Ų buried · 44 hydrogen bonds · protein-protein
• C–D · 813 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

• 5ESU · Crystal Structure of M. tuberculosis MenD bound to Mg2+ and Covalent Intermediate II (a… · the same entry in another collection · chain A against A, TM-score 1.00
• P9WK11 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P9WK11
• Elsewhere: RCSB PDB 5ESU · PDBe 5ESU · UniProt P9WK11