Crystal structure of streptomyces tokunonesis tokk with hydroxycobalamin, 5'-deoxyadenosine, methionine, and (2R)- pantetheinylated carbapenam

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
• B12 · Cobalamin · ligand · 2 copies · chains A, B
• MET · Methionine · ligand · 2 copies · chains A, B
• 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
• WCD · (2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · chains A
• K · Potassium ion · metal · 4 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1032 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

• 7KDY · Crystal structure of Streptomyces toku sis TokK with hydroxycobalamin, 5'-deoxyadenosine… · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A6B9HEI0
• Elsewhere: RCSB PDB 7KDY · PDBe 7KDY · UniProt A0A6B9HEI0