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

• AXB · N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide · ligand · 2 copies · chains A, B
• HAE · Acetohydroxamic acid · ligand · chains A
• 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

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

Interfaces

1 interface between chains.

• A–B · 195 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 3DPF · 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 3DPF · PDBe 3DPF · UniProt P22894