› 5gie

X-ray diffraction
2.39Å resolution

Crystal structure of VDR in complex with DLAM-4P (P21 form)

Released:
DOI: 10.2210/pdb5gie/pdb
PDB entry 5gie coloured by chain, front view.
PDB entry 5gie coloured by chain, side view.
PDB entry 5gie coloured by chain, top view.
Source organisms:
Primary publication:
Regulation of the vitamin D receptor by vitamin D lactam derivatives.
Asano L, Waku T, Abe R, Kuwabara N, Ito I, Yanagisawa J, Nagasawa K, Shimizu T
FEBS Lett 590 3270-9 (2016)
PMID: 27500498

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 Chains: A, D
Molecule details ›
Chains: A, D
Length: 256 amino acids
Theoretical weight: 29.09 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13053 (Residues: 117-419; Coverage: 61%)
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 Chains: C, E
Molecule details ›
Chains: C, E
Length: 10 amino acids
Theoretical weight: 1.21 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15648 (Residues: 641-650; Coverage: 1%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2

Ligands and Environments

1 bound ligand:
Ligand VDP 2 x VDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 65.364Å b: 42.077Å c: 96.802Å
α: 90° β: 94.55° γ: 90°
R-values:
R R work R free
0.209 0.207 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Vitamin D and Its Synthetic Analogs.
Maestro et al. (2019)
1 more