› 6h8t

X-ray diffraction
2.1Å resolution

Crystal structure of Papain modify by achiral Ru(II)complex

Released:
DOI: 10.2210/pdb6h8t/pdb
PDB entry 6h8t coloured by chain, front view.
PDB entry 6h8t coloured by chain, side view.
PDB entry 6h8t coloured by chain, top view.
Source organism: Carica papaya
Primary publication:
Crystallographic evidence for unexpected selective tyrosine hydroxylations in an aerated achiral Ru-papain conjugate.
Cherrier MV, Amara P, Talbi B, Salmain M, Fontecilla-Camps JC
Metallomics 10 1452-1459 (2018)
PMID: 30175357

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 analysis Details

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

Ligands and Environments

6 bound ligands:
Ligand ACT 9 x ACT
Ligand CL 1 x CL
Ligand YXZ 1 x YXZ
Ligand YXX 1 x YXX
Ligand SO4 1 x SO4
Ligand NA 1 x NA
2 modified residues:
Ligand OMX 1 x OMX
Ligand TXY 1 x TXY

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 61.03Å b: 74.85Å c: 86.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.192 0.249
Expression system: Carica papaya

Quick links

Citations

1 mention without citation

The Future of Carica papaya Leaf Extract as an Herbal Medicine Product.
Hariono et al. (2021)