1BY4 Gene Regulation Dna date Oct 22, 1998
title Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna
authors Q.Zhao, S.A.Chasse, S.Devarakonda, M.L.Sierk, B.Ahvazi, P.B.Sigler, F.Rastinejad
compound source
Molecule: Protein (Retinoic Acid Receptor Rxr-Alpha)
Chain: A, B, C, D
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Ctpapgpgptpcpapapapgpgptpcpapg)-3');
Chain: E, G
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Cptpgpapcpcptptptpgpapcpcptpa)-3');
Chain: F, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
70.930 33.650 101.400 90.00 89.95 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand ZN enzyme
related structures by homologous chain: 1R0O, 2NLL
A, D, C, B

Primary referenceStructural basis of RXR-DNA interactions., Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B, Rastinejad F, J Mol Biol 2000 Feb 18;296(2):509-20. PMID:10669605
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (1by4.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (1by4.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 1BY4
  • CSU: Contacts of Structural Units for 1BY4
  • Likely Quarternary Molecular Structure file(s) for 1BY4
  • Retrieve 1BY4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BY4 from S2C, [Save to disk]
  • View 1BY4 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 1BY4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1BY4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1by4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1by4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1by4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1by4d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1by4 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: [1by4_G] [1by4_C] [1by4] [1by4_H] [1by4_B] [1by4_E] [1by4_F] [1by4_D] [1by4_A]
  • SWISS-PROT database: [P19793]
  • Domain organization of [RXRA_HUMAN] by SWISSPFAM
  • Domain found in 1BY4: [ZnF_C4 ] by SMART
  • Other resources with information on 1BY4
  • Community annotation for 1BY4 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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