1RK3	Hormone Growth Factor Receptor	date	Nov 20, 2003
title	Crystal Structure Of The Rat Vitamin D Receptor Ligand Bindi Complexed With 1,25-Dihydroxyvitamin D3 And A Synthetic Pep Containing The Nr2 Box Of Drip 205
authors	J.L.Vanhooke, M.M Benning, C.B.Bauer, J.W.Pike, 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) Codonplus 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, Trip2, P53 Regulatory Prote Vitamin D Receptor-Interacting Protein Complex Component Dr Activator-Recruited Cofactor 205 Kda Component, Arc205; Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 1 2 1	R_factor 0.190 R_Free 0.243
crystal cell	length a length b length c angle alpha angle beta angle gamma 154.726 44.154 42.072 90.00 96.13 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	VDX	enzyme
related structures	by homologous chain: 1RKH, 1S19
Gene Ontology	Chain Function Process Component A
Primary reference	Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide., Vanhooke JL, Benning MM, Bauer CB, Pike JW, DeLuca HF, Biochemistry 2004 Apr 13;43(14):4101-10. PMID:15065852

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk] Biological Unit Coordinates (1rk3.pdb1.gz) 42 Kb Biological Unit Coordinates (1rk3.pdb2.gz) 83 Kb LPC: Ligand-Protein Contacts for 1RK3 CSU: Contacts of Structural Units for 1RK3 Likely Quarternary Molecular Structure file(s) for 1RK3 Structure Factors (104 Kb) Retrieve 1RK3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RK3 from S2C, [Save to disk] Re-refined 1rk3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RK3 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 1RK3

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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 1RK3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rk3a_, region A [Jmol] [rasmolscript] [script source] 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: [1rk3] [1rk3_C] [1rk3_A] SWISS-PROT database: [Q15648] [P13053] Domain organization of [MED1_HUMAN] [VDR_RAT] by SWISSPFAM Domain found in 1RK3: [HOLI ] by SMART

Other resources with information on 1RK3

Community annotation for 1RK3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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