› 5z5o

X-ray diffraction
1.92Å resolution

Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K

Released:
DOI: 10.2210/pdb5z5o/pdb
PDB entry 5z5o coloured by chain, front view.
PDB entry 5z5o coloured by chain, side view.
PDB entry 5z5o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T.
Roy S, Das Chakraborty S, Biswas S
FEBS J 285 4265-4280 (2018)
PMID: 30199612

Function and Biology Details

Reaction catalysed: 
Broad proteolytic activity. With small-molecule substrates and inhibitors, the major determinant of specificity is P2, which is preferably Leu, Met > Phe, and not Arg.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154997 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cathepsin K Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 37.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P43235 (Residues: 16-329; Coverage: 100%)
Gene names: CTSK, CTSO, CTSO2
Sequence domains:
Structure domains: Cysteine proteinases
Cathepsin K Chain: B
Molecule details ›
Chain: B
Length: 94 amino acids
Theoretical weight: 11.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P43235 (Residues: 16-88; Coverage: 23%)
Gene names: CTSK, CTSO, CTSO2
Sequence domains: Cathepsin propeptide inhibitor domain (I29)

Ligands and Environments

7 bound ligands:
Ligand GOL 8 x GOL
Ligand EDO 16 x EDO
Ligand SO4 5 x SO4
Ligand PEG 7 x PEG
Ligand CL 1 x CL
Ligand NA 1 x NA
Ligand MPD 3 x MPD
1 modified residue:
Ligand SEB 1 x SEB

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 50.1Å b: 67.27Å c: 82.87Å
α: 90° β: 91.83° γ: 90°
R-values:
R R work R free
0.164 0.162 0.204
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Normal Mode Analysis as a Routine Part of a Structural Investigation.
Bauer et al. (2019)
1 more

1 mention without citation

Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T.
Roy et al. (2018)