› 5z3j

X-ray diffraction
1.7Å resolution

Crystal Structure of Abrin A chain (Recombinant) in complex with Nicotinamide at 1.7 Angstroms

Released:
DOI: 10.2210/pdb5z3j/pdb
PDB entry 5z3j coloured by chain, front view.
PDB entry 5z3j coloured by chain, side view.
PDB entry 5z3j coloured by chain, top view.
Source organism: Abrus precatorius
Primary publication:
Structural basis for neutralization of cytotoxic abrin by monoclonal antibody D6F10.
Bansia H, Bagaria S, Karande AA, Ramakumar S
FEBS J 286 1003-1029 (2019)
PMID: 30521151

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-145672 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Abrin-a A chain Chain: A
Molecule details ›
Chain: A
Length: 265 amino acids
Theoretical weight: 29.71 KDa
Source organism: Abrus precatorius
Expression system: Escherichia coli
UniProt:
  • Canonical: P11140 (Residues: 1-251; Coverage: 48%)
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand IMD 1 x IMD
Ligand NCA 1 x NCA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR-H
Spacegroup: P212121
Unit cell:
a: 41.66Å b: 74.08Å c: 82.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.222
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Homology Modeling of Antibody Variable Regions: Methods and Applications.
Bansia et al. (2023)
1 more

1 mention without citation

Structural basis for neutralization of cytotoxic abrin by monoclonal antibody D6F10.
Bansia et al. (2019)