› 4fvl

X-ray diffraction
2.44Å resolution

Human collagenase 3 (MMP-13) full form with peptides from pro-domain

Released:
DOI: 10.2210/pdb4fvl/pdb
PDB entry 4fvl coloured by chain, front view.
PDB entry 4fvl coloured by chain, side view.
PDB entry 4fvl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain.
Stura EA, Visse R, Cuniasse P, Dive V, Nagase H
FASEB J 27 4395-405 (2013)
PMID: 23913860

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155287 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Collagenase 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 368 amino acids
Theoretical weight: 42.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45452 (Residues: 104-471; Coverage: 81%)
Gene name: MMP13
Sequence domains:
Structure domains:
Collagenase 3 Chains: C, D
Molecule details ›
Chains: C, D
Length: 20 amino acids
Theoretical weight: 2.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45452 (Residues: 31-50; Coverage: 4%)
Gene name: MMP13
Sequence domains: Putative peptidoglycan binding domain

Ligands and Environments

6 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 10 x CA
Ligand CL 3 x CL
Ligand GOL 10 x GOL
Ligand PGO 28 x PGO
Ligand PEG 9 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2221
Unit cell:
a: 125.78Å b: 157.27Å c: 105.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.166 0.223
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Matrix metalloproteinase interactions with collagen and elastin.
Van Doren SR. (2015)
4 more

3 mentions without citation

Peptides and Peptidomimetics as Inhibitors of Enzymes Involved in Fibrillar Collagen Degradation.
LedwoĊ„ et al. (2021)
2 more