2HBH image
Deposition Date 2006-06-14
Release Date 2007-05-01
Last Version Date 2023-10-25
Entry Detail
PDB ID:
2HBH
Keywords:
GENE REGULATION
Title:
Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide
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:
2.65 Å
R-Value Free:
0.26
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 65 2 2
2HBH 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
XE4
Primary Citation
Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol
Arch.Biochem.Biophys. 460 172 176 (2007)
PMID: 17346665 DOI: 10.1016/j.abb.2007.01.031

Abstact

The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.

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Chemical

Disease

Primary Citation of related structures
1DB1
2HC4
2HCD