Crystal structure of an inactive mutant of mmp-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate with a fluorine atom.

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 20% strand (DSSP).

Ligands and binding sites

• 8MC · (7-methoxy-2-oxo-2H-chromen-4-yl)acetic acid · ligand · 2 copies · chains P, A, Q, B
• ZN · Zinc ion · metal · 4 copies · chains P, A, Q, B
• CA · Calcium ion · metal · 3 copies · chains A, B
• SR · Strontium ion · metal · 3 copies · chains A, B
• NA · Sodium ion · metal · 3 copies · chains A, B, Q
• NH2 · Amino group · ion · 2 copies · chains P, Q
• AZI · Azide ion · ion · 2 copies · chains P, A, Q, B
• EDO · 1,2-ethanediol · additive · 7 copies · chains A, P, Q, B
• PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
• GOL · Glycerol · additive · chains P, A

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

3 interfaces between chains.

• Q–B · 717 Ų buried · 9 hydrogen bonds · protein-protein
• P–A · 707 Ų buried · 9 hydrogen bonds · protein-protein
• A–B · 653 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

• 4JQG · Crystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a… · the same entry in another collection · chain Q against Q, 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 0.97

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