› 5i3m

X-ray diffraction
2.17Å resolution

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).

Released:
DOI: 10.2210/pdb5i3m/pdb
PDB entry 5i3m coloured by chain, front view.
PDB entry 5i3m coloured by chain, side view.
PDB entry 5i3m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors.
Nuti E, Cuffaro D, D'Andrea F, Rosalia L, Tepshi L, Fabbi M, Carbotti G, Ferrini S, Santamaria S, Camodeca C, Ciccone L, Orlandini E, Nencetti S, Stura EA, Dive V, Rossello A
ChemMedChem 11 1626-37 (2016)
PMID: 27356908

Function and Biology Details

Reaction catalysed: 
Hydrolysis of soluble and insoluble elastin (1). Specific cleavages are also produced at -Ala(14)-|-Leu- and -Tyr(16)-|-Leu- in the B chain of insulin (2).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153971 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Macrophage metalloelastase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 159 amino acids
Theoretical weight: 17.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P39900 (Residues: 106-263; Coverage: 35%)
Gene names: HME, MMP12
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

7 bound ligands:
Ligand 67F 4 x 67F
Ligand ZN 8 x ZN
Ligand CA 12 x CA
Ligand DMS 2 x DMS
Ligand PGO 2 x PGO
Ligand DIO 3 x DIO
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 63.72Å b: 63.14Å c: 78.92Å
α: 90° β: 103.09° γ: 90°
R-values:
R R work R free
0.208 0.206 0.253
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Digestive Inflammation: Role of Proteolytic Dysregulation.
Mariaule et al. (2021)
2 more