1KB4 Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element date
authors Shaffer, P.L., Gewirth, D.T.
compound source
R_Free 0.2720000
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand ZN enzyme
related structures by homologous chain: 1KB2, 1YNW
A, B

Primary referenceStructural basis of VDR-DNA interactions on direct repeat response elements., Shaffer PL, Gewirth DT, EMBO J 2002 May 1;21(9):2242-52. PMID:11980721
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1kb4.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 1KB4
  • CSU: Contacts of Structural Units for 1KB4
  • Likely Quarternary Molecular Structure file(s) for 1KB4
  • Structure Factors (126 Kb)
  • Retrieve 1KB4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KB4 from S2C, [Save to disk]
  • Re-refined 1kb4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KB4 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 1KB4
  • 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 1KB4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kb4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kb4b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1kb4 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: [1kb4_A] [1kb4_B] [1kb4] [1kb4_D] [1kb4_C]
  • 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 1KB4: [ZnF_C4 ] by SMART
  • Other resources with information on 1KB4
  • Community annotation for 1KB4 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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