2HC4 image
Deposition Date 2006-06-15
Release Date 2007-05-01
Last Version Date 2023-10-25
Entry Detail
PDB ID:
2HC4
Keywords:
GENE REGULATION
Title:
Crystal structure of the LBD of VDR of Danio rerio in complex with calcitriol
Biological Source:
Source Organism:
Danio rerio (Taxon ID: 7955)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.20 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 65 2 2
2HC4 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Vitamin D receptor
Gene (Uniprot):vdra
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Danio rerio
UniProt ID:Q9PTN2 Pfam ID:PF00104
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SRC-1 from Nuclear receptor coactivator 1
Gene (Uniprot):NCOA1
Chain IDs:B
Chain Length:15
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15788 EC:2.3.1.48
Ligand Molecules
VDX
Primary Citation
Adaptability of the Vitamin D nuclear receptor to the synthetic ligand Gemini: remodelling the LBP with one side chain rotation
J.Steroid Biochem.Mol.Biol. 103 235 242 (2007)
PMID: 17218092 DOI: 10.1016/j.jsbmb.2006.12.003

Abstact

The crystal structure of the ligand binding domain (LBD) of the wild-type Vitamin D receptor (VDR) of zebrafish bound to Gemini, a synthetic agonist ligand with two identical side chains branching at carbon 20 reveals a ligand-dependent structural rearrangement of the ligand binding pocket (LBP). The rotation of a Leu side chain opens the access to a channel that can accommodate the second side chain of the ligand. The 25% increase of the LBP's volume does not alter the essential agonist features of VDR. The possibility to adapt the LBP to novel ligands with different chemistry and/or structure opens new perspectives in the design of more specifically targeted ligands.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1DB1
2HBH
2HCD