› 5j56

X-ray diffraction
1.8Å resolution

RTA-V1C7

Released:
DOI: 10.2210/pdb5j56/pdb
Model geometry
Fit model/data
PDB entry 5j56 coloured by chain, front view.
PDB entry 5j56 coloured by chain, side view.
PDB entry 5j56 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Analysis of Single Domain Antibodies Bound to a Second Neutralizing Hot Spot on Ricin Toxin's Enzymatic Subunit.
Rudolph MJ, Vance DJ, Cassidy MS, Rong Y, Mantis NJ
J Biol Chem 292 872-883 (2017)
PMID: 27903650

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208807 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ricin A chain Chain: A
Molecule details ›
Chain: A
Length: 268 amino acids
Theoretical weight: 30.07 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02879 (Residues: 36-302; Coverage: 49%)
Sequence domains: Ribosome inactivating protein
Structure domains:
VHH single chain antibody V1C7 Chain: B
Molecule details ›
Chain: B
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

4 bound ligands:
Ligand PG4 1 x PG4
Ligand ACY 2 x ACY
Ligand EDO 1 x EDO
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3221
Unit cell:
a: 64.768Å b: 64.768Å c: 215.016Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.173 0.21
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein-Protein Interaction Analysis, and Protein Function Exploration.
Beghein et al. (2017)
2 more

4 mentions without citation

High-Resolution Epitope Positioning of a Large Collection of Neutralizing and Nonneutralizing Single-Domain Antibodies on the Enzymatic and Binding Subunits of Ricin Toxin.
Vance et al. (2017)
3 more