› 2d1n

X-ray diffraction
2.37Å resolution

Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor

Released:
DOI: 10.2210/pdb2d1n/pdb
Model geometry
Fit model/data
PDB entry 2d1n coloured by chain, front view.
PDB entry 2d1n coloured by chain, side view.
PDB entry 2d1n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453.
Kohno T, Hochigai H, Yamashita E, Tsukihara T, Kanaoka M
Biochem Biophys Res Commun 344 315-22 (2006)
PMID: 16603129

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155286 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Collagenase 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 166 amino acids
Theoretical weight: 18.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45452 (Residues: 104-269; Coverage: 37%)
Gene name: MMP13
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand CA 6 x CA
Ligand FA4 2 x FA4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU RU200
Spacegroup: P32
Unit cell:
a: 96.47Å b: 96.47Å c: 67.52Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.221 0.218 0.239
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Matrix metalloproteinases in exercise and obesity.
Jaoude et al. (2016)
8 other articles

5 mentions without citation

Premna odorata: Seasonal Metabolic Variation in the Essential Oil Composition of Its Leaf and Verification of Its Anti-Ageing Potential via In Vitro Assays and Molecular Modelling.
Altyar et al. (2020)
4 more