› 3h5k

X-ray diffraction
1.45Å resolution

Crystal structure of the ribosome inactivating protein PDL1

Released:
DOI: 10.2210/pdb3h5k/pdb
PDB entry 3h5k coloured by chain, front view.
PDB entry 3h5k coloured by chain, side view.
PDB entry 3h5k coloured by chain, top view.
Source organism: Phytolacca dioica
Primary publication:
Crystal structure of PD-L1, a ribosome inactivating protein from Phytolacca dioica L. leaves with the property to induce DNA cleavage.
Ruggiero A, Di Maro A, Severino V, Chambery A, Berisio R
Biopolymers 91 1135-42 (2009)
PMID: 19452522

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-160918 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosome-inactivating protein PD-L1/PD-L2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 261 amino acids
Theoretical weight: 29.25 KDa
Source organism: Phytolacca dioica
UniProt:
  • Canonical: P84853 (Residues: 1-261; Coverage: 100%)
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NAG 2 x NAG
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: C2
Unit cell:
a: 161.011Å b: 34.735Å c: 120.63Å
α: 90° β: 127.99° γ: 90°
R-values:
R R work R free
0.198 0.196 0.242

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Citations

2 review citations

Biological activities of ribosome-inactivating proteins and their possible applications as antimicrobial, anticancer, and anti-pest agents and in neuroscience research.
Akkouh et al. (2015)
1 more

1 mention without citation

Strategies to Improve the Clinical Utility of Saporin-Based Targeted Toxins.
Giansanti et al. (2018)