› 6imf

X-ray diffraction
2.3Å resolution

Crystal structure of TOXIN/ANTITOXIN complex

Released:
DOI: 10.2210/pdb6imf/pdb
PDB entry 6imf coloured by chain, front view.
PDB entry 6imf coloured by chain, side view.
PDB entry 6imf coloured by chain, top view.
Source organism: Protobothrops flavoviridis
Primary publication:
Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake.
Shioi N, Tadokoro T, Shioi S, Okabe Y, Matsubara H, Kita S, Ose T, Kuroki K, Terada S, Maenaka K
J Biol Chem 294 1250-1256 (2019)
PMID: 30504218

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108466 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cysteine-rich venom protein triflin Chain: A
Molecule details ›
Chain: A
Length: 221 amino acids
Theoretical weight: 24.83 KDa
Source organism: Protobothrops flavoviridis
UniProt:
  • Canonical: Q8JI39 (Residues: 20-240; Coverage: 100%)
Sequence domains:
Structure domains:
Small serum protein 2 Chain: B
Molecule details ›
Chain: B
Length: 109 amino acids
Theoretical weight: 12.14 KDa
Source organism: Protobothrops flavoviridis
UniProt:
  • Canonical: A7VN14 (Residues: 1-109; Coverage: 100%)
Sequence domains: Beta-microseminoprotein (PSP-94)

Ligands and Environments

2 bound ligands:
Ligand MES 1 x MES
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2
Unit cell:
a: 111.166Å b: 48.113Å c: 75.028Å
α: 90° β: 102.61° γ: 90°
R-values:
R R work R free
0.187 0.186 0.219

Quick links

Citations

2 citation in other articles

Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions.
Jia et al. (2021)
1 more

5 mentions without citation

Animal toxins - Nature's evolutionary-refined toolkit for basic research and drug discovery.
Herzig et al. (2020)
4 more