› 4zbv

X-ray diffraction
2Å resolution

Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with benzyl T-antigen

Released:
DOI: 10.2210/pdb4zbv/pdb
PDB entry 4zbv coloured by chain, front view.
PDB entry 4zbv coloured by chain, side view.
PDB entry 4zbv coloured by chain, top view.
Source organism: Momordica charantia
Primary publication:
Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure.
Chandran T, Sharma A, Vijayan M
J Biosci 40 929-41 (2015)
PMID: 26648038

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-110641 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Ribosome-inactivating protein Chain: A
Molecule details ›
Chain: A
Length: 247 amino acids
Theoretical weight: 27.64 KDa
Source organism: Momordica charantia
UniProt:
  • Canonical: B7X8M2 (Residues: 24-270; Coverage: 47%)
Gene names: LOC111023549, MCL1
Sequence domains: Ribosome inactivating protein
Structure domains:
Ribosome-inactivating protein Chain: B
Molecule details ›
Chain: B
Length: 261 amino acids
Theoretical weight: 29.02 KDa
Source organism: Momordica charantia
UniProt:
  • Canonical: B7X8M2 (Residues: 287-547; Coverage: 50%)
Gene names: LOC111023549, MCL1
Sequence domains: Ricin-type beta-trefoil lectin domain
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
8 bound ligands:
Ligand NAG 2 x NAG
Ligand PO4 1 x PO4
Ligand BMA 1 x BMA
Ligand EDO 1 x EDO
Ligand PGE 1 x PGE
Ligand GAL 1 x GAL
Ligand A2G 1 x A2G
Ligand MBN 1 x MBN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21212
Unit cell:
a: 130.31Å b: 138.4Å c: 44.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.231 0.266

Quick links

Citations

1 review citation

Plant Lectins Targeting O-Glycans at the Cell Surface as Tools for Cancer Diagnosis, Prognosis and Therapy.
Poiroux et al. (2017)
1 other article