1YNW	Transcription Dna	date	Jan 25, 2005
title	Crystal Structure Of Vitamin D Receptor And 9-Cis Retinoic A Receptor Dna-Binding Domains Bound To A Dr3 Response Elemen
authors	P.L.Shaffer, D.T.Gewirth
compound		source
Molecule: 5'-D(Tptpapgpgptpcpapcpgpapapgpgpt -3'; Chain: C Engineered: Yes Other_details: Dr3 Response Element		Synthetic: Yes
Molecule: 5'-D(Tptptpgpapcpcptptpcpgptpgpapc -3'; Chain: D Engineered: Yes Other_details: Dr3 Response Element		Synthetic: Yes
Molecule: Vitamin D3 Receptor Chain: A Fragment: Dna-Binding Domain (Residues 16-125) Synonym: Vdr; 1,25-Dihydroxyvitamin D3 Receptor Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vdr, Nr1i1 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(Rpkls)
Molecule: Retinoic Acid Receptor Rxr-Alpha Chain: B Fragment: Dna-Binding Domain (Residues 130-228) Synonym: 9-Cis Retinoic Acid Receptor; Retinoid X Receptor Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rxra, Nr2b1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-Rxr(Sane)
symmetry	Space Group: C 1 2 1	R_factor 0.232 R_Free 0.283
crystal cell	length a length b length c angle alpha angle beta angle gamma 123.104 57.049 73.438 90.00 110.31 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	ZN	enzyme
note	1YNW (Molecule of the Month:pdb155)
related structures	by homologous chain: 1CIT, 1KB4, 1RXR
Gene Ontology	Chain Function Process Component A B
Primary reference	Structural analysis of RXR-VDR interactions on DR3 DNA., Shaffer PL, Gewirth DT, J Steroid Biochem Mol Biol 2004 May;89-90(1-5):215-9. PMID:15225774

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk] Biological Unit Coordinates (1ynw.pdb1.gz) 42 Kb LPC: Ligand-Protein Contacts for 1YNW CSU: Contacts of Structural Units for 1YNW Likely Quarternary Molecular Structure file(s) for 1YNW Structure Factors (189 Kb) Retrieve 1YNW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YNW from S2C, [Save to disk] Re-refined 1ynw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YNW 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 1YNW

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 3D motif for 1YNW, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ynw_B] [1ynw_D] [1ynw] [1ynw_A] [1ynw_C] SWISS-PROT database: [P19793] [P11473] Belongs to the vitamin d3 receptor (vdr) family according to TCDB. Domain organization of [RXRA_HUMAN] [VDR_HUMAN] by SWISSPFAM Domain found in 1YNW: [ZnF_C4 ] by SMART

Other resources with information on 1YNW

Community annotation for 1YNW at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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