› 6ic5

X-ray diffraction
2Å resolution

Human cathepsin-C in complex with dipeptidyl cyclopropyl nitrile inhibitor 2

Released:
DOI: 10.2210/pdb6ic5/pdb
PDB entry 6ic5 coloured by chain, front view.
PDB entry 6ic5 coloured by chain, side view.
PDB entry 6ic5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C.
Korkmaz B, Lesner A, Wysocka M, Gieldon A, Håkansson M, Gauthier F, Logan DT, Jenne DE, Lauritzen C, Pedersen J
Biochem Pharmacol 164 349-367 (2019)
PMID: 30978322

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, except when Xaa is Arg or Lys, or Yaa or Zaa is Pro.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156846 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Dipeptidyl peptidase 1 exclusion domain chain Chain: A
Molecule details ›
Chain: A
Length: 119 amino acids
Theoretical weight: 13.5 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P53634 (Residues: 25-143; Coverage: 27%)
Gene names: CPPI, CTSC
Sequence domains: Cathepsin C exclusion domain
Structure domains: Cathepsin C, exclusion domain
Dipeptidyl peptidase 1 heavy chain Chain: B
Molecule details ›
Chain: B
Length: 162 amino acids
Theoretical weight: 18.3 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P53634 (Residues: 230-391; Coverage: 37%)
Gene names: CPPI, CTSC
Sequence domains: Papain family cysteine protease
Structure domains: Cysteine proteinases
Dipeptidyl peptidase 1 light chain Chain: C
Molecule details ›
Chain: C
Length: 69 amino acids
Theoretical weight: 7.58 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P53634 (Residues: 395-463; Coverage: 16%)
Gene names: CPPI, CTSC
Structure domains: Cysteine proteinases. Chain C

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 2 x NAG
Ligand CL 1 x CL
Ligand HB5 1 x HB5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER X8 PROTEUM
Spacegroup: I222
Unit cell:
a: 86.975Å b: 88.329Å c: 115.183Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.152 0.198
Expression system: Trichoplusia ni

Quick links

Citations

5 review citations

Cathepsins in the Pathophysiology of Mucopolysaccharidoses: New Perspectives for Therapy.
De Pasquale et al. (2020)
4 more