2o4j Summary


Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205

The structure was published by Vanhooke, J.L., Tadi, B.P., Benning, M.M., Plum, L.A., and Deluca, H.F., in 2007 in a paper entitled "New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.74 Å and deposited in 2006.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely Vitamin D3 receptor and Peroxisome proliferator-activated receptor-binding protein.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):

Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Vitamin D3 receptor P13053 (116-423) (VDR_RAT)search Rattus norvegicussearch < 90% 292 82%
C Peroxisome proliferator-activated receptor-binding protein Q15648 (640-652) (MED1_HUMAN)search Homo sapienssearch < 90% 13 92%

This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P13053 (116 - 423) Vitamin D3 receptor Rattus norvegicus
Q15648 (640 - 652) Peroxisome proliferator-activated receptor-binding protein

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A Nuclear receptor ligand-binding domainsearch Retinoid X Receptorsearch Ligand-binding domain of nuclear hormone receptorsearch

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
A (P13053) DNA bindingsearch sequence-specific DNA binding transcription factor activitysearch steroid hormone receptor activitysearch thyroid hormone receptor activitysearch nucleussearch regulation of transcription, DNA-templatedsearch steroid hormone mediated signaling pathwaysearch

Chain InterPro annotation
A Nuclear hormone receptor, ligand-binding, coresearch Steroid hormone receptorsearch Thyroid hormone receptorsearch Nuclear hormone receptor, ligand-bindingsearch