Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3

Summary for 5B41

DescriptorVitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2-methylenecyclohexane-1,3-diol, ... (4 entities in total)
Functional Keywordstranscription, vitamin d3, vdr, vdre, rxr, co-factors
Biological sourceRattus norvegicus (Rat)
Cellular locationNucleus P13053 Q15648
Total number of polymer chains2
Total molecular weight32582.57
Anami, Y.,Itoh, T.,Yamamoto, K. (deposition date: 2016-03-23, release date: 2016-12-07)
Primary citation
Anami, Y.,Shimizu, N.,Ekimoto, T.,Egawa, D.,Itoh, T.,Ikeguchi, M.,Yamamoto, K.
Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics
J.Med.Chem., 59:7888-7900, 2016
PubMed: 27535484 (PDB entries with the same primary citation)
DOI: 10.1021/acs.jmedchem.6b00682
MImport into Mendeley
Experimental method

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2461303.1%4.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution