3A3Z Gene Regulation date Jun 25, 2009
title Crystal Structure Of The Human Vdr Ligand Binding Domain Bou Synthetic Agonist Compound 2alpha-Methyl-Amcr277a(C23s)
authors Y.Sato, P.Antony, T.Huet, R.Sigueiro, N.Rochel, D.Moras, Structura Proteomics In Europe 2 (Spine-2)
compound source
Molecule: Vitamin D3 Receptor
Chain: X
Fragment: Ligand Binding Domain, Unp Residues 118-427
Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor, Nuclear Re Subfamily 1 Group I Member 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.297 51.688 133.092 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.72 Å
ligand 2MV, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
X


Primary referenceStructure-Function Relationships and Crystal Structures of the Vitamin D Receptor Bound 2alpha-Methyl-(20S,23S)- and 2alpha-Methyl-(20S,23R)-epoxymethano-1alpha,25-dihydroxyvitamin D(3)., Antony P, Sigueiro R, Huet T, Sato Y, Ramalanjaona N, Rodrigues LC, Mourino A, Moras D, Rochel N, J Med Chem. 2010 Jan 13. PMID:20070104
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (3a3z.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3A3Z
  • CSU: Contacts of Structural Units for 3A3Z
  • Structure Factors (252 Kb)
  • Retrieve 3A3Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A3Z from S2C, [Save to disk]
  • Re-refined 3a3z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A3Z in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3A3Z
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3A3Z, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a3z_X] [3a3z]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3A3Z: [HOLI ] by SMART
  • Other resources with information on 3A3Z
  • Community annotation for 3A3Z at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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