› 5v39

X-ray diffraction
2.2Å resolution

Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM

Released:
DOI: 10.2210/pdb5v39/pdb
PDB entry 5v39 coloured by chain, front view.
PDB entry 5v39 coloured by chain, side view.
PDB entry 5v39 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions.
Zheng J, Chang MR, Stites RE, Wang Y, Bruning JB, Pascal BD, Novick SJ, Garcia-Ordonez RD, Stayrook KR, Chalmers MJ, Dodge JA, Griffin PR
Nat Commun 8 923 (2017)
PMID: 29030554

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: 257 amino acids
Theoretical weight: 29.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11473 (Residues: 119-425; Coverage: 60%)
Gene names: NR1I1, VDR
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor

Ligands and Environments

1 bound ligand:
Ligand 8VM 1 x 8VM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 44Å b: 52.67Å c: 105.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.167 0.235
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.
James et al. (2022)
2 more

1 mention without citation

HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions.
Zheng et al. (2017)