Crystal structure of mycinamicin VIII C21 methyl hydroxylase mycci from micromonospora griseorubida bound to mycinamicin VIII

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).

Ligands and binding sites

• SPD · Spermidine · ligand · 3 copies · chains A
• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• MY8 · Mycinamicin VIII · ligand · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 608 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 5FOI · Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora… · the same entry in another collection · chain A against A, TM-score 1.00
• Q83WF5 · AlphaFold monomer V2.0 prediction for mycinamicin VIII C21 methyl hydroxylase (Q83WF5) · 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 Q83WF5
• Elsewhere: RCSB PDB 5FOI · PDBe 5FOI · UniProt Q83WF5