1DB1 Gene Regulation date Nov 02, 1999
title Crystal Structure Of The Nuclear Receptor For Vitamin D Comp Vitamin D
authors N.Rochel, J.M.Wurtz, A.Mitschler, B.Klaholz, D.Moras
compound source
Molecule: Vitamin D Nuclear Receptor
Chain: A
Fragment: Ligand Binding Domain
Synonym: Vdr
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.214
length a length b length c angle alpha angle beta angle gamma
45.193 52.443 133.286 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand VDX enzyme
note 1DB1 (Molecule of the Month:pdb155)
related structures by homologous chain: 1IE8, 1TXI

Primary referenceThe crystal structure of the nuclear receptor for vitamin D bound to its natural ligand., Rochel N, Wurtz JM, Mitschler A, Klaholz B, Moras D, Mol Cell 2000 Jan;5(1):173-9. PMID:10678179
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (1db1.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 1DB1
  • CSU: Contacts of Structural Units for 1DB1
  • Likely Quarternary Molecular Structure file(s) for 1DB1
  • Structure Factors (246 Kb)
  • Retrieve 1DB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DB1 from S2C, [Save to disk]
  • Re-refined 1db1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DB1 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 1DB1
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1DB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1db1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1k1db1, region B:1-52,B:385-460 [Jmol] [rasmolscript] [script source]
        - Domain d1c1db1, region B:149-348 [Jmol] [rasmolscript] [script source]
  • Fold representative 1db1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1db1] [1db1_A]
  • SWISS-PROT database: [P11473]
  • Belongs to the vitamin d3 receptor (vdr) family according to TCDB.
  • Domain organization of [VDR_HUMAN] by SWISSPFAM
  • Domain found in 1DB1: [HOLI ] by SMART
  • Other resources with information on 1DB1
  • Community annotation for 1DB1 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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