› 2q8w

X-ray diffraction
1.7Å resolution

Crystal structure of PAP-S1aci, a pokeweed antiviral protein from seeds of Phytolacca acinosa

Released:
DOI: 10.2210/pdb2q8w/pdb
PDB entry 2q8w coloured by chain, front view.
PDB entry 2q8w coloured by chain, side view.
PDB entry 2q8w coloured by chain, top view.
Source organism: Phytolacca acinosa
Entry authors: Hogg T, Hilgenfeld R

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112152 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
rRNA N-glycosylase Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 29.32 KDa
Source organism: Phytolacca acinosa
UniProt:
  • Canonical: D0VWY1 (Residues: 1-261; Coverage: 100%)
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: I222
Unit cell:
a: 78.63Å b: 84.19Å c: 90.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.169 0.211

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