› 1k3b

X-ray diffraction
2.15Å resolution

Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): Exclusion Domain Added to an Endopeptidase Framework Creates the Machine for Activation of Granular Serine Proteases

Released:
DOI: 10.2210/pdb1k3b/pdb
PDB entry 1k3b coloured by chain, front view.
PDB entry 1k3b coloured by chain, side view.
PDB entry 1k3b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases.
Turk D, Janjić V, Stern I, Podobnik M, Lamba D, Dahl SW, Lauritzen C, Pedersen J, Turk V, Turk B
EMBO J 20 6570-82 (2001)
PMID: 11726493

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 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 (3 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: 164 amino acids
Theoretical weight: 18.49 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P53634 (Residues: 231-394; 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

3 bound ligands:
Ligand NAG 1 x NAG
Ligand SO4 3 x SO4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: I222
Unit cell:
a: 87.154Å b: 88.031Å c: 114.609Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.19 0.231
Expression system: Trichoplusia ni

Quick links

Citations

46 review citations

Targeting proteases: successes, failures and future prospects.
Turk B. (2006)
45 more

11 mentions without citation

Cysteine cathepsins: from structure, function and regulation to new frontiers.
Turk et al. (2012)
10 more