3VT6	Hormone Receptor	date	May 19, 2012
title	Crystal Structure Of Rat Vdr-Lbd With 2-Substituted-16-Ene-2 1alpha,25-Dihydroxy-26,27-Dimethyl-19-Norvitamin D3
authors	M.Nakabayashi, M.Shimizu, T.Ikura, N.Ito
compound		source
Molecule: Vitamin D3 Receptor Chain: A Fragment: Unp Residues 116-423 Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor, Nuclear Re Subfamily 1 Group I Member 1; Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Rats Organism_taxid: 10116 Gene: Nr1i1, Vdr Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: C41 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet14b
Molecule: Coactivator Peptide Drip Chain: C Engineered: Yes		Synthetic: Yes Other_details: Peptide Synthesis
symmetry	Space Group: C 1 2 1	R_factor 0.210 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 153.734 42.724 42.271 90.00 95.55 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	5YI	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal Structures of Hereditary Vitamin D-Resistant Rickets-Associated Vitamin D Receptor Mutants R270L and W282R Bound to 1,25-Dihydroxyvitamin D and Synthetic Ligands., Nakabayashi M, Tsukahara Y, Iwasaki-Miyamoto Y, Mihori-Shimazaki M, Yamada S, Inaba S, Oda M, Shimizu M, Makishima M, Tokiwa H, Ikura T, Ito N, J Med Chem. 2013 Aug 29. PMID:23944708

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk] Biological Unit Coordinates (3vt6.pdb1.gz) 42 Kb Biological Unit Coordinates (3vt6.pdb2.gz) 40 Kb LPC: Ligand-Protein Contacts for 3VT6 CSU: Contacts of Structural Units for 3VT6 Structure Factors (146 Kb) Retrieve 3VT6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3VT6 from S2C, [Save to disk] Re-refined 3vt6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3VT6 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 3VT6

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 3VT6, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3vt6_A] [3vt6] [3vt6_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3VT6: [HOLI ] by SMART

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