› 1bp4

X-ray diffraction
2.2Å resolution

USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES.

Released:
DOI: 10.2210/pdb1bp4/pdb
PDB entry 1bp4 coloured by chain, front view.
PDB entry 1bp4 coloured by chain, side view.
PDB entry 1bp4 coloured by chain, top view.
Source organism: Carica papaya
Primary publication:
Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites.
LaLonde JM, Zhao B, Smith WW, Janson CA, DesJarlais RL, Tomaszek TA, Carr TJ, Thompson SK, Oh HJ, Yamashita DS, Veber DF, Abdel-Meguid SS
J Med Chem 41 4567-76 (1998)
PMID: 9804696

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins with broad specificity for peptide bonds, but preference for an amino acid bearing a large hydrophobic side chain at the P2 position. Does not accept Val in P1'.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133539 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Papain Chain: A
Molecule details ›
Chain: A
Length: 212 amino acids
Theoretical weight: 23.45 KDa
Source organism: Carica papaya
UniProt:
  • Canonical: P00784 (Residues: 134-345; Coverage: 65%)
Sequence domains: Papain family cysteine protease
Structure domains: Cysteine proteinases

Ligands and Environments

1 bound ligand:
Ligand ALD 1 x ALD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SIEMENS
Spacegroup: C2
Unit cell:
a: 100.54Å b: 50.74Å c: 62.28Å
α: 90° β: 99.9° γ: 90°
R-values:
R R work R free
0.19 0.19 0.24

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Citations

19 citation in other articles

Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain.
Huang et al. (2001)
18 more

8 mentions without citation

Structure determinants defining the specificity of papain-like cysteine proteases.
Petushkova et al. (2022)
7 more