› 3a78

X-ray diffraction
1.9Å resolution

Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3

Released:
DOI: 10.2210/pdb3a78/pdb
PDB entry 3a78 coloured by chain, front view.
PDB entry 3a78 coloured by chain, side view.
PDB entry 3a78 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Sato Y, Sigueiro R, Antony P, Rochel N, Moras D

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145848 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 263 amino acids
Theoretical weight: 29.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11473 (Residues: 118-427; Coverage: 61%)
Gene names: NR1I1, VDR
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor

Ligands and Environments

2 bound ligands:
Ligand 3EV 1 x 3EV
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 44.889Å b: 51.12Å c: 132.196Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.203
Expression system: Escherichia coli BL21(DE3)

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