› 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 entry 4g0d coloured by chain, front view.
PDB entry 4g0d coloured by chain, side view.
PDB entry 4g0d 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, 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

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

4 mentions without citation

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