› 1pip

X-ray diffraction
1.7Å resolution

CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS

Released:
DOI: 10.2210/pdb1pip/pdb
PDB entry 1pip coloured by chain, front view.
PDB entry 1pip coloured by chain, side view.
PDB entry 1pip coloured by chain, top view.
Source organism: Carica papaya
Primary publication:
Crystal structure of papain-succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide complex at 1.7-A resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors.
Yamamoto A, Tomoo K, Doi M, Ohishi H, Inoue M, Ishida T, Yamamoto D, Tsuboi S, Okamoto H, Okada Y
Biochemistry 31 11305-9 (1992)
PMID: 1445868

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133544 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Papain Chain: A
Molecule details ›
Chain: A
Length: 212 amino acids
Theoretical weight: 23.45 KDa
Source organism: Carica papaya
Expression system: Not provided
UniProt:
  • Canonical: P00784 (Residues: 134-345; Coverage: 65%)
Sequence domains: Papain family cysteine protease
Structure domains: Cysteine proteinases
SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE Chain: B
Molecule details ›
Chain: B
Length: 7 amino acids
Theoretical weight: 707 Da
Source organism: Carica papaya
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 43.09Å b: 102.3Å c: 49.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 not available
Expression system: Not provided

Quick links

Citations

3 review citations

The lysosomal cysteine proteases.
McGrath ME. (1999)
2 more

6 mentions without citation

A contemporary review on the important role of in silico approaches for managing different aspects of COVID-19 crisis.
Moradi et al. (2022)
5 more