› 2rg9

X-ray diffraction
1.95Å resolution

Crystal structure of viscum album mistletoe lectin I in native state at 1.95 A resolution, comparison of structure active site conformation in ricin and in viscumin

Released:
DOI: 10.2210/pdb2rg9/pdb
PDB entry 2rg9 coloured by chain, front view.
PDB entry 2rg9 coloured by chain, side view.
PDB entry 2rg9 coloured by chain, top view.
Source organism: Viscum album
Entry authors: Karpechenko NU, Timofeev VI, Gabdoulkhakov AG, Mikhailov AM

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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160520 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Beta-galactoside-specific lectin 1 chain A isoform 1 Chain: A
Molecule details ›
Chain: A
Length: 249 amino acids
Theoretical weight: 27.62 KDa
Source organism: Viscum album
Expression system: Not provided
UniProt:
  • Canonical: P81446 (Residues: 34-282; Coverage: 47%)
Sequence domains: Ribosome inactivating protein
Structure domains:
Beta-galactoside-specific lectin 1 chain B Chain: B
Molecule details ›
Chain: B
Length: 263 amino acids
Theoretical weight: 28.75 KDa
Source organism: Viscum album
Expression system: Not provided
UniProt:
  • Canonical: P81446 (Residues: 302-564; Coverage: 50%)
Sequence domains: Ricin-type beta-trefoil lectin domain
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)

Ligands and Environments

5 bound ligands:
Ligand NAG 4 x NAG
Ligand SO4 1 x SO4
Ligand AZI 3 x AZI
Ligand CL 2 x CL
Ligand GOL 15 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P6522
Unit cell:
a: 106.95Å b: 106.95Å c: 310.95Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.222 0.239
Expression system: Not provided

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