› 1tfm

X-ray diffraction
2.8Å resolution

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

Released:
DOI: 10.2210/pdb1tfm/pdb
PDB entry 1tfm coloured by chain, front view.
PDB entry 1tfm coloured by chain, side view.
PDB entry 1tfm coloured by chain, top view.
Source organism: Viscum album
Entry authors: Mishra V, Bilgrami S, Paramasivam M, Yadav S, Sharma RS, Kaur P, Srinivasan A, Babu CR, Singh TP

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 domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179780 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (6 distinct):
Beta-galactoside-specific lectin 4 chain A Chain: A
Molecule details ›
Chain: A
Length: 240 amino acids
Theoretical weight: 26.57 KDa
Source organism: Viscum album
UniProt:
  • Canonical: Q6ITZ3 (Residues: 1-240; Coverage: 46%)
Sequence domains: Ribosome inactivating protein
Structure domains:
Beta-galactoside-specific lectin 4 chain B Chain: B
Molecule details ›
Chain: B
Length: 255 amino acids
Theoretical weight: 27.63 KDa
Source organism: Viscum album
UniProt:
  • Canonical: Q6ITZ3 (Residues: 266-520; Coverage: 49%)
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
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GAL, BGC
Carbohydrate polymer
3 bound ligands:
Ligand NAG 1 x NAG
Ligand P6C 1 x P6C
Ligand GAL 1 x GAL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P6522
Unit cell:
a: 109.422Å b: 109.422Å c: 309.798Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.24 0.234 0.289

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