› 8wm0

X-ray diffraction
2.8Å resolution

Crystal structure of TNIK-thiopeptide wTP3 complex

Released:
DOI: 10.2210/pdb8wm0/pdb
PDB entry 8wm0 coloured by chain, front view.
PDB entry 8wm0 coloured by chain, side view.
PDB entry 8wm0 coloured by chain, top view.
Source organisms:
Primary publication:
A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides.
Vinogradov AA, Zhang Y, Hamada K, Kobayashi S, Ogata K, Sengoku T, Goto Y, Suga H
J Am Chem Soc (2024)
PMID: 38491946

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-553914 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
TRAF2 and NCK-interacting protein kinase Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 35.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
THIOPEPTIDE wTP3 Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.86 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ADN 1 x ADN
3 modified residues:
Ligand TPO 2 x TPO
Ligand SAR 2 x SAR
Ligand DHA 4 x DHA

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P65
Unit cell:
a: 53.72Å b: 53.72Å c: 220.17Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.233 0.227 0.285
Expression systems:
  • Escherichia coli
  • Not provided

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