› 6jez

X-ray diffraction
2.3Å resolution

Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization

Released:
DOI: 10.2210/pdb6jez/pdb
PDB entry 6jez coloured by chain, front view.
PDB entry 6jez coloured by chain, side view.
PDB entry 6jez coloured by chain, top view.
Source organisms:
Primary publication:
Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.
Kojima H, Fujita Y, Takeuchi R, Ikebe Y, Ohashi N, Yamamoto K, Itoh T
Cell Chem Biol 27 334-349.e11 (2020)
PMID: 31991094

Function and Biology Details

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-146463 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 30.6 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13053 (Residues: 116-163, 213-423; Coverage: 61%)
Gene names: Nr1i1, Vdr
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Mediator of RNA polymerase II transcription subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15648 (Residues: 640-652; Coverage: 1%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2

Ligands and Environments

2 bound ligands:
Ligand YSV 1 x YSV
Ligand EJO 1 x EJO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 153.93Å b: 43.39Å c: 42Å
α: 90° β: 95.3° γ: 90°
R-values:
R R work R free
0.205 0.202 0.256
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors.
Bianco et al. (2020)
1 more