1KB2 Transcription Dna date Nov 05, 2001
title Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element
authors P.L.Shaffer, D.T.Gewirth
compound source
Molecule: 5'- D(Cpapcpgpgptptpcpapcpgpapgpgptptpcpa)- 3';
Chain: C
Engineered: Yes
Other_details: Mouse Osteopontin (Spp) Response Element
Synthetic: Yes

Molecule: 5'- D(Tpgpapapcpcptpcpgptpgpapapcpcpgptpg)- 3';
Chain: D
Engineered: Yes
Other_details: Mouse Osteopontin (Spp) Response Element

Synthetic: Yes

Molecule: Vitamin D3 Receptor
Chain: A, B
Fragment: Dna-Binding Domain (Residues 16-125)
Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vdr
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a-Vdr-N1-Rplks
symmetry Space Group: P 43 21 2
R_factor 0.226 R_Free 0.289
length a length b length c angle alpha angle beta angle gamma
62.140 62.140 241.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand ZN enzyme
note 1KB2 (Molecule of the Month:pdb155)
related structures by homologous chain: 1KB4, 1KB6
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] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1kb2.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 1KB2
  • CSU: Contacts of Structural Units for 1KB2
  • Likely Quarternary Molecular Structure file(s) for 1KB2
  • Structure Factors (138 Kb)
  • Retrieve 1KB2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KB2 from S2C, [Save to disk]
  • Re-refined 1kb2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KB2 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 1KB2
  • 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 1KB2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kb2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kb2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1p1kb2, region B:323-437 [Jmol] [rasmolscript] [script source]
        - Domain d1w1kb2, region B:6-273 [Jmol] [rasmolscript] [script source]
  • Fold representative 1kb2 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: [1kb2_C] [1kb2_A] [1kb2_D] [1kb2_B] [1kb2]
  • 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 1KB2: [ZnF_C4 ] by SMART
  • Other resources with information on 1KB2
  • Community annotation for 1KB2 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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