1KB4 Transcription Dna date Nov 05, 2001
title Crystal Structure Of Vdr Dna-Binding Domain Bound To A Canonical Direct Repeat With Three Base Pair Spacer (Dr3) Response Element
authors P.L.Shaffer, D.T.Gewirth
compound source
Molecule: 5'- D(Cpapcpapgpgptpcpapcpgpapapgpgptpcpa)- 3';
Chain: C
Engineered: Yes
Other_details: Canonical Direct Repeat With 3 Base Pair Spacer (Dr3) Response Element;
 Synthetic: Yes

Molecule: 5'- D(Tpgpapcpcptptpcpgptpgpapcpcptpgptpg)- 3';
Chain: D
Engineered: Yes
Other_details: Canonical Direct Repeat With 3 Base Pair Spacer (Dr3) 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 0.214 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.500 61.500 241.970 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ZN enzyme
related structures by homologous chain: 1KB2, 1YNW
Gene
Ontology
ChainFunctionProcessComponent
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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • 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]
  • Domain organization of [VDR_HUMAN] by SWISSPFAM
  • Domain found in 1KB4: [ZnF_C4 ] by SMART
  • Alignments of the sequence of 1KB4 with the sequences similar proteins can be viewed for 1KB4's classification [VDR_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [VDR_HUMAN] at ProtoMap. Click on the Cluster number.
    • 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.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2010
    Bioinformatics Unit
    Weizmann Institute of Science