Crystal structure of an mmp twin inhibitor complexing two mmp-9 catalytic domains

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 18% strand (DSSP).

Ligands and binding sites

• BCN · Bicine · ligand · 3 copies · chains A, B
• 0Y3 · N,N'-bis(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide · ligand · chains A, B
• CA · Calcium ion · metal · 5 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B
• ACT · Acetate ion · additive · 4 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 419 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 4H2E · Crystal structure of an MMP twin inhibitor complexing two MMP-9 catalytic domains · the same entry in another collection · chain A against A, TM-score 1.00
• P14780 · AlphaFold monomer V2.0 prediction for matrix metalloproteinase-9 (P14780) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P14780
• Elsewhere: RCSB PDB 4H2E · PDBe 4H2E · UniProt P14780