› 4g0d

X-ray diffraction
2.54Å resolution

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

Released:
DOI: 10.2210/pdb4g0d/pdb
PDB 4g0d coloured by chain and viewed from the front.
PDB 4g0d coloured by chain and viewed from the side.
PDB 4g0d coloured by chain and viewed from the top.
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. (2013)
PMID: 23913860

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Collagenase 3 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
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: W, X, Y, Z
Molecule details ›
Chains: W, X, Y, Z
Length: 26 amino acids
Theoretical weight: 3.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45452 (Residues: 25-50; Coverage: 6%)
Gene name: MMP13
Sequence domains: Putative peptidoglycan binding domain

Ligands and Environments

6 bound ligands:
Ligand ZN 8 x ZN
Ligand CA 23 x CA
Ligand CL 8 x CL
Ligand PGO 38 x PGO
Ligand PEG 4 x PEG
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 101.26Å b: 105.9Å c: 101.18Å
α: 90° β: 102.11° γ: 90°
R-values:
R R work R free
0.172 0.169 0.241
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Recent advances in understanding the regulation of metalloproteinases.
Young et al. (2019)
4 more

4 mentions without citation

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