1BY4 Gene Regulation Dna date Oct 22, 1998
title Structure And Mechanism Of The Homodimeric Assembly Of The R
authors Q.Zhao, S.A.Chasse, S.Devarakonda, M.L.Sierk, B.Ahvazi, P.B.Sigle F.Rastinejad
compound source
Molecule: Dna (5'-D(Ctpapgpgptpcpapapapgpgptp 3');
Chain: E, G
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

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
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.284
crystal
cell
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
Gene
Ontology
ChainFunctionProcessComponent
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] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (1by4.pdb1.gz) 42 Kb
  • Biological Unit Coordinates (1by4.pdb2.gz) 41 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
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server 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]
  • 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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