2ZMJ	Transcription	date	Apr 19, 2008
title	Crystal Structure Of Rat Vitamin D Receptor Bound To Adamant D Analogs: Structural Basis For Vitamin D Receptor Antagoni Partial Agonism
authors	M.Nakabayashi, S.Yamada, T.Tanaka, M.Igarashi, N.Yoshimoto, T.Iku M.Makishima, H.Tokiwa, H.F.Deluca, M.Shimizu
compound		source
Molecule: Vitamin D3 Receptor Chain: A Fragment: Ligand Binding Domain, Unp Residues 116-423 Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor, Nuclear Re Subfamily 1 Group I Member 1; Engineered: Yes Mutation: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Rat Organism_taxid: 10116 Gene: Vdr, Nr1i1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: C41 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-14b
Molecule: Mediator Of Rna Polymerase II Transcription Subun Chain: C Fragment: Drip 205 Nr2 Box Peptide, Unp Residues 624-636 Synonym: Mediator Complex Subunit 1, Peroxisome Proliferato Activated Receptor; Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide
symmetry	Space Group: C 1 2 1	R_factor 0.222 R_Free 0.271
crystal cell	length a length b length c angle alpha angle beta angle gamma 153.730 43.242 41.953 90.00 95.50 90.00
method	X-Ray Diffraction	resolution	2.35 Å
ligand	MI4	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal Structures of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and Partial Agonism., Nakabayashi M, Yamada S, Yoshimoto N, Tanaka T, Igarashi M, Ikura T, Ito N, Makishima M, Tokiwa H, Deluca HF, Shimizu M, J Med Chem. 2008 Aug 19. PMID:18710208

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk] Biological Unit Coordinates (2zmj.pdb1.gz) 42 Kb LPC: Ligand-Protein Contacts for 2ZMJ CSU: Contacts of Structural Units for 2ZMJ Likely Quarternary Molecular Structure file(s) for 2ZMJ Structure Factors (157 Kb) Retrieve 2ZMJ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ZMJ from S2C, [Save to disk] Re-refined 2zmj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ZMJ 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 2ZMJ

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 2ZMJ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2zmj_A] [2zmj] [2zmj_C] SWISS-PROT database: [P13053] Domain organization of [VDR_RAT] by SWISSPFAM Domain found in 2ZMJ: [HOLI ] by SMART

Other resources with information on 2ZMJ

Community annotation for 2ZMJ at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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