Crystal structure of trmd from pseudomonas aeruginosa in complex with active-site inhibitor

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).

Ligands and binding sites

• BWR · ~{N}-[[4-[(4-azanylpiperidin-1-yl) methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2, 3-d]pyrimidine-5-carboxamide · ligand · chains A, B
• SAM · S-adenosylmethionine · ligand · chains A, B
• PO4 · Phosphate ion · ion · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3585 Ų buried · 79 hydrogen bonds · protein-protein

Compared structures

• 6JOE · Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site… · the same entry in another collection · chain A against A, TM-score 1.00
• Q02RL6 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (Q02RL6) · a predicted model of the same protein · chain A 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 Q02RL6
• Elsewhere: RCSB PDB 6JOE · PDBe 6JOE · UniProt Q02RL6