2O4J	Hormone Growth Factor Receptor	date	Dec 04, 2006
title	Crystal Structure Of Rat Vitamin D Receptor Ligand Binding D Complexed With Vitiii 17-20z And The Nr2 Box Of Drip 205
authors	J.L.Vanhooke, M.M.Benning, H.F.Deluca
compound		source
Molecule: Vitamin D3 Receptor Chain: A Fragment: Ligand Binding Domain Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor Engineered: Yes Mutation: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Gene: Vdr, Nr1i1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl-21(De3) Codon Plus Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-29b
Molecule: Peroxisome Proliferator-Activated Receptor-Bindin Chain: C Fragment: Drip 205 Nr2 Box Peptide Synonym: Pbp, Ppar-Binding Protein, Thyroid Hormone Recepto Associated Protein Complex 220 Kda Component, Trap220, Thyr Receptor-Interacting Protein 2, Trip-2, P53 Regulatory Prot Vitamin D Receptor-Interacting Protein Complex Component Dr Activator- Recruited Cofactor 205 Kda Component, Arc205; Engineered: Yes		Synthetic: Yes Other_details: Synthesized At Uw-Madison Biotechnology Cent
symmetry	Space Group: C 1 2 1	R_factor 0.199 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 155.500 42.400 41.900 90.00 96.50 90.00
method	X-Ray Diffraction	resolution	1.74 Å
ligand	VD4	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations., Vanhooke JL, Tadi BP, Benning MM, Plum LA, Deluca HF, Arch Biochem Biophys. 2006 Dec 12;. PMID:17227670

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk] Biological Unit Coordinates (2o4j.pdb1.gz) 45 Kb Biological Unit Coordinates (2o4j.pdb2.gz) 88 Kb LPC: Ligand-Protein Contacts for 2O4J CSU: Contacts of Structural Units for 2O4J Likely Quarternary Molecular Structure file(s) for 2O4J Structure Factors (213 Kb) Retrieve 2O4J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2O4J from S2C, [Save to disk] Re-refined 2o4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2O4J 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 2O4J

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 2O4J, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2o4j] [2o4j_C] [2o4j_A] SWISS-PROT database: [Q15648] [P13053] Domain organization of [MED1_HUMAN] [VDR_RAT] by SWISSPFAM Domain found in 2O4J: [HOLI ] by SMART

Other resources with information on 2O4J

Community annotation for 2O4J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---