Crystal structure of the catalytic domain of mmp-12 in complex with a selective sugar-conjugated thiourea-linked carboxylate zinc-chelator water-soluble inhibitor (DC31).

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 17% strand (DSSP).

Ligands and binding sites

• 67F · (2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]carbamothioyl}amino)ethyl](biphenyl-4-ylsulfonyl)amino}-3-methylbutanoic acid (non-preferred name) · ligand · 4 copies · chains A, C, B, D
• CA · Calcium ion · metal · 12 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
• DIO · 1,4-diethylene dioxide · additive · 3 copies · chains B, C
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, D
• PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · chains 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

5 interfaces between chains.

• A–C · 349 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 293 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 232 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 173 Ų buried · 0 hydrogen bonds · protein-protein
• B–C · 65 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5I3M · 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 5I3M · PDBe 5I3M · UniProt P39900