PDBsum entry 2hbh

Go to PDB code: 
protein ligands links
Gene regulation PDB id
Protein chain
239 a.a. *
Waters ×74
* Residue conservation analysis
PDB id:
Name: 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
Structure: Vitamin d receptor. Chain: a. Fragment: ligand binding domain. Engineered: yes. Src-1 from nuclear receptor coactivator 1. Chain: b. Synonym: ncoa-1, steroid receptor coactivator 1, src-1, rip160, protein hin-2, ny-ren-52 antigen. Engineered: yes
Source: Danio rerio. Zebrafish. Organism_taxid: 7955. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: this sequence occurs naturally in humans
2.65Å     R-factor:   0.203     R-free:   0.261
Authors: N.Rochel,S.Hourai,D.Moras
Key ref: N.Rochel et al. (2007). 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. PubMed id: 17346665 DOI: 10.1016/
14-Jun-06     Release date:   01-May-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9PTN2  (VDRA_DANRE) -  Vitamin D3 receptor A
453 a.a.
239 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   2 terms 
  Biochemical function     DNA binding     4 terms  


DOI no: 10.1016/ Arch Biochem Biophys 460:172-176 (2007)
PubMed id: 17346665  
Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol.
N.Rochel, S.Hourai, X.Pérez-García, A.Rumbo, A.Mourino, D.Moras.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19223058 T.Kaya, N.Swamy, K.S.Persons, S.Ray, S.C.Mohr, and R.Ray (2009).
Covalent labeling of nuclear vitamin D receptor with affinity labeling reagents containing a cross-linking probe at three different positions of the parent ligand: structural and biochemical implications.
  Bioorg Chem, 37, 57-63.  
18844850 H.F.DeLuca (2008).
Evolution of our understanding of vitamin D.
  Nutr Rev, 66, S73-S87.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.