› 5zwf

X-ray diffraction
2.1Å resolution

Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a enone with a beta methyl group via conjugate addition reaction

Released:
DOI: 10.2210/pdb5zwf/pdb
PDB entry 5zwf coloured by chain, front view.
PDB entry 5zwf coloured by chain, side view.
PDB entry 5zwf coloured by chain, top view.
Source organisms:
Primary publication:
Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands.
Yoshizawa M, Itoh T, Hori T, Kato A, Anami Y, Yoshimoto N, Yamamoto K
J Med Chem 61 6339-6349 (2018)
PMID: 29936834

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: 116-423; Coverage: 62%)
Gene names: Nr1i1, Vdr
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X 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: synthetic construct
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

1 bound ligand:
Ligand 9KR 1 x 9KR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 153.56Å b: 41.73Å c: 42.02Å
α: 90° β: 96.22° γ: 90°
R-values:
R R work R free
0.235 0.234 0.25
Expression systems:
  • Escherichia coli
  • synthetic construct

Quick links

Citations

2 review citations

Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation.
Zhang et al. (2019)
1 more