Crystal structure of the complex between mmp-8 and a non-zinc chelating inhibitor

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 17% strand (DSSP).

Ligands and binding sites

• AXA · (5S)-5-(2-amino-2-oxoethyl)-4-oxo-N-[(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-6-yl)methyl]-3,4,5,6,7,8-hexahydro[1]benzothieno[2,3-d]pyrimidine-2-carboxamide · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 379 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 3DNG · Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• P22894 · AlphaFold monomer V2.0 prediction for neutrophil collagenase (P22894) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P22894
• Elsewhere: RCSB PDB 3DNG · PDBe 3DNG · UniProt P22894