2ZLC Hormone date Apr 04, 2008
title 2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26,27-Dimet Norvitamin D3 Analogs: Synthesis, Biological Evaluation And Structure
authors M.Shimizu, Y.Miyamoto, M.Nakabayashi, H.Masuno, T.Ikura, N.Ito
compound source
Molecule: Vitamin D3 Receptor
Chain: A
Fragment: Vdr-Lbd, Unp Residues 116-423
Synonym: Ligand Binding Domain Of Vitamin D Receptor, Vdr, Dihydroxyvitamin D3 Receptor, Nuclear Receptor Subfamily 1 Member 1;
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Vdr, Nr1i1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b

Molecule: Coactivator Peptide Drip
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Peptide Synthesis
symmetry Space Group: C 1 2 1
R_factor 0.225 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
153.859 41.998 41.951 90.00 96.06 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand VDX enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvita min D(3) analogs: Synthesis, biological evaluation, and crystal structure., Shimizu M, Miyamoto Y, Takaku H, Matsuo M, Nakabayashi M, Masuno H, Udagawa N, Deluca HF, Ikura T, Ito N, Bioorg Med Chem. 2008 May 27;. PMID:18539034
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (2zlc.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 2ZLC
  • CSU: Contacts of Structural Units for 2ZLC
  • Likely Quarternary Molecular Structure file(s) for 2ZLC
  • Structure Factors (248 Kb)
  • Retrieve 2ZLC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZLC from S2C, [Save to disk]
  • Re-refined 2zlc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZLC 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 2ZLC
  • 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 2ZLC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zlc] [2zlc_C] [2zlc_A]
  • SWISS-PROT database: [P13053]
  • Domain organization of [VDR_RAT] by SWISSPFAM
  • Domain found in 2ZLC: [HOLI ] by SMART
  • Other resources with information on 2ZLC
  • Community annotation for 2ZLC 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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