› 1lyb

X-ray diffraction
2.5Å resolution

CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Released:
DOI: 10.2210/pdb1lyb/pdb
PDB entry 1lyb coloured by chain, front view.
PDB entry 1lyb coloured by chain, side view.
PDB entry 1lyb coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design.
Baldwin ET, Bhat TN, Gulnik S, Hosur MV, Sowder RC, Cachau RE, Collins J, Silva AM, Erickson JW
Proc Natl Acad Sci U S A 90 6796-800 (1993)
PMID: 8393577

Function and Biology Details

Reaction catalysed: 
Specificity similar to, but narrower than, that of pepsin A. Does not cleave the 4-Gln-|-His-5 bond in B chain of insulin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
hetero hexamer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139522 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Cathepsin D light chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 97 amino acids
Theoretical weight: 10.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P07339 (Residues: 65-161; Coverage: 25%)
Gene names: CPSD, CTSD
Structure domains: Acid Proteases
Cathepsin D heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 241 amino acids
Theoretical weight: 26.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P07339 (Residues: 170-410; Coverage: 62%)
Gene names: CPSD, CTSD
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases
PEPSTATIN Chains: I, J
Molecule details ›
Chains: I, J
Length: 6 amino acids
Theoretical weight: 686 Da
Source organism: Streptomyces argenteolus subsp. toyonakensis
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P65
Unit cell:
a: 125.9Å b: 125.9Å c: 104.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.179 not available
Expression system: Not provided

Quick links

Citations

18 review citations

Cathepsin D--many functions of one aspartic protease.
Benes et al. (2008)
17 more

15 mentions without citation

Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases.
Goettig P. (2016)
14 more