2HBH Gene Regulation date Jun 14, 2006
title Crystal Structure Of Vitamin D Nuclear Receptor Ligand Bindi Bound To A Locked Side-Chain Analog Of Calcitriol And Src-1
authors N.Rochel, S.Hourai, D.Moras
compound source
Molecule: Vitamin D Receptor
Chain: A
Fragment: Ligand Binding Domain
Engineered: Yes
Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: Src-1 From Nuclear Receptor Coactivator 1
Chain: B
Synonym: Ncoa-1, Steroid Receptor Coactivator 1, Src-1, Rip Protein Hin-2, Ny-Ren-52 Antigen;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans
symmetry Space Group: P 65 2 2
R_factor 0.203 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.682 65.682 265.096 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.65 Å
ligand XE4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol., Rochel N, Hourai S, Perez-Garcia X, Rumbo A, Mourino A, Moras D, Arch Biochem Biophys. 2007 Apr 15;460(2):172-6. Epub 2007 Feb 20. PMID:17346665
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (2hbh.pdb1.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 2HBH
  • CSU: Contacts of Structural Units for 2HBH
  • Likely Quarternary Molecular Structure file(s) for 2HBH
  • Structure Factors (80 Kb)
  • Retrieve 2HBH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HBH from S2C, [Save to disk]
  • Re-refined 2hbh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HBH 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 2HBH
  • 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 2HBH, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hbh_B] [2hbh] [2hbh_A]
  • SWISS-PROT database: [Q15788] [Q9PTN2]
  • Domain organization of [NCOA1_HUMAN] [VDRA_DANRE] by SWISSPFAM
  • Domain found in 2HBH: [HOLI ] by SMART
  • Other resources with information on 2HBH
  • Community annotation for 2HBH 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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