› 4jij

X-ray diffraction
1.7Å resolution

Crystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate

Released:
DOI: 10.2210/pdb4jij/pdb
PDB entry 4jij coloured by chain, front view.
PDB entry 4jij coloured by chain, side view.
PDB entry 4jij coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Halogen bonding controls selectivity of FRET substrate probes for MMP-9.
Tranchant I, Vera L, Czarny B, Amoura M, Cassar E, Beau F, Stura EA, Dive V
Chem Biol 21 408-13 (2014)
PMID: 24583051

Function and Biology Details

Reaction catalysed: 
Cleavage of gelatin types I and V and collagen types IV and V.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147086 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2) Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 9 amino acids
Theoretical weight: 1.25 KDa
Source organism: Homo sapiens
Expression system: Not provided
67 kDa matrix metalloproteinase-9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 164 amino acids
Theoretical weight: 18.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14780 (Residues: 107-444; Coverage: 24%)
Gene names: CLG4B, MMP9
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

8 bound ligands:
Ligand AZI 2 x AZI
Ligand ZN 4 x ZN
Ligand CA 2 x CA
Ligand SR 4 x SR
Ligand PGO 2 x PGO
Ligand EDO 4 x EDO
Ligand PEG 1 x PEG
Ligand GOL 2 x GOL
2 modified residues:
Ligand PHI 2 x PHI
Ligand DNW 2 x DNW

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 34.2Å b: 57.4Å c: 172.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.16 0.195
Expression systems:
  • Not provided
  • Escherichia coli

Quick links

Citations

1 review citation

TIMPs: versatile extracellular regulators in cancer.
Jackson et al. (2017)
7 other articles

10 mentions without citation

Non-Canonical Amino Acids in Analyses of Protease Structure and Function.
Goettig et al. (2023)
9 more