Crystal structure of the catalytic domain of mmp-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelating water-soluble inhibitor (DC24).

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 17% strand (DSSP).

Ligands and binding sites

• V24 · N-[([1,1'-biphenyl]-4-yl)sulfonyl]-N-({1-[3,4,6-tri-O-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1H-1,2,3-triazol-4-yl}methyl)-D-valine · 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
• PGO · S-1,2-propanediol · additive · 2 copies · chains A, D
• EDO · 1,2-ethanediol · additive · chains C
• DMS · Dimethyl sulfoxide · additive · chains D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 335 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 276 Ų buried · 1 hydrogen bond · protein-protein
• C–D · 228 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 199 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 54 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5I2Z · Crystal structure of the catalytic domain of MMP-12 in complex with a selective… · 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 P39900
• Elsewhere: RCSB PDB 5I2Z · PDBe 5I2Z · UniProt P39900