1A6Y Transcription Dna date Mar 04, 1998
title Reverba Orphan Nuclear Receptordna Complex
authors Q.Zhao, S.Khorasanizadeh, F.Rastinejad
compound source
Molecule: Dna (5'- D(Cpapapcptpapgpgptpcpapcp(5it) Papgpgptpcpapg)-3');
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Cptpgpapcpcptpapgptpgpapcpcptpapgptptp G)-3');
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Orphan Nuclear Receptor Nr1d1
Chain: A, B
Fragment: Dna Binding Domain Consists Of Residues A 101 To A 164, B 101 To B 164;
Synonym: Thyroid Hormone Receptor-Related Protein Rev-Erba- Alpha, Reverb, Reverba Orphan Nuclear Receptor, V-Erba Related Protein Ear-1;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pgex
symmetry Space Group: P 1
R_factor 0.192 R_Free 0.288
length a length b length c angle alpha angle beta angle gamma
38.670 45.690 47.950 75.16 80.64 85.58
method X-Ray Diffractionresolution 2.30 Å
ligand 5IU, ZN enzyme
related structures by homologous chain: 1DSZ, 1GA5
A, B

Primary referenceStructural elements of an orphan nuclear receptor-DNA complex., Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F, Mol Cell 1998 May;1(6):849-61. PMID:9660968
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (1a6y.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 1A6Y
  • CSU: Contacts of Structural Units for 1A6Y
  • Likely Quarternary Molecular Structure file(s) for 1A6Y
  • Structure Factors (90 Kb)
  • Retrieve 1A6Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1A6Y from S2C, [Save to disk]
  • Re-refined 1a6y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1A6Y 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 1A6Y
  • 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 1A6Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1a6ya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1a6yb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1a6y 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: [1a6y_D] [1a6y_C] [1a6y] [1a6y_B] [1a6y_A]
  • SWISS-PROT database: [P20393]
  • Domain organization of [NR1D1_HUMAN] by SWISSPFAM
  • Domain found in 1A6Y: [ZnF_C4 ] by SMART
  • Other resources with information on 1A6Y
  • Community annotation for 1A6Y 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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