3OAP Transcription date Aug 05, 2010
title Crystal Structure Of Human Retinoid X Receptor Alpha-Ligand Domain Complex With 9-Cis Retinoic Acid And The Coactivator Grip-1
authors G.Xia, C.D.Smith, D.D.Muccio
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A
Fragment: Hrxralpha-Lbd, Unp Residues 228-458
Synonym: Retinoid X Receptor Alpha, Nuclear Receptor Subfam Group B Member 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rxra, Nr2b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nuclear Receptor Coactivator 2
Chain: B
Fragment: Grip-1, Unp Residues 686-696
Synonym: Ncoa-2, Transcriptional Intermediary Factor 2, Hti E Basic Helix-Loop-Helix Protein 75, Bhlhe75, Glucocorticoi Interacting Protein-1 (Grip-1);
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 43 21 2
R_factor 0.204 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.831 65.831 111.856 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand REA BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructure, Energetics and Dynamics of Binding Coactivator Peptide to Human Retinoid X Receptor Alpha Ligand Binding Domain Complex with 9-cis-Retinoic Acid., Xia G, Boerma LJ, Cox BD, Qiu C, Kang S, Smith CD, Renfrow MB, Muccio DD, Biochemistry. 2010 Nov 4. PMID:21049972
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (3oap.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 3OAP
  • CSU: Contacts of Structural Units for 3OAP
  • Structure Factors (232 Kb)
  • Retrieve 3OAP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OAP from S2C, [Save to disk]
  • Re-refined 3oap structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OAP 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 3OAP
  • 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 3OAP, from MSDmotif at EBI
  • Fold representative 3oap from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3oap_B] [3oap_A] [3oap]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3OAP with the sequences similar proteins can be viewed for 3OAP's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3OAP
  • Community annotation for 3OAP 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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