Crystal structure of the catalytic domain of mmp-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelator water-soluble inhibitor (DC32).

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 17% strand (DSSP).

Ligands and binding sites

• 67M · (2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}oxy)propyl]-1H-1,2,3-triazol-4-yl}methyl)(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid (non-preferred name) · ligand · 4 copies · chains A, B, C, D
• CA · Calcium ion · metal · 12 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 23 copies · chains A, C, B, D
• PGO · S-1,2-propanediol · additive · 6 copies · chains B, C, A, D
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, C

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

4 interfaces between chains.

• A–C · 299 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 235 Ų buried · 0 hydrogen bonds · protein-protein
• A–B · 233 Ų buried · 0 hydrogen bonds · protein-protein
• B–D · 180 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 5I43 · Crystal structure of the catalytic domain of MMP-12 in complex with a selective… · the same entry in another collection · chain B against B, 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 P39900
• Elsewhere: RCSB PDB 5I43 · PDBe 5I43 · UniProt P39900