3KDU	Hormone Receptor	date	Oct 23, 2009
title	Crystal Structure Of Peroxisome Proliferator-Activatedecepto (Pparalpha) Complex With N-3-((2-(4-Chlorophenyl)-5-Methyl- Oxazol-4-Yl)Methoxy)Benzyl)-N-((4-Methylphenoxy)Carbonyl)Gl
authors	J.K.Muckelbauer
compound		source
Molecule: Peroxisome Proliferator-Activated Receptor Alpha Chain: A, B Fragment: Ligand-Binding Domain: Unp Residues 196-468 Synonym: Ppar-Alpha, Nuclear Receptor Subfamily 1 Group C M Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ppara, Nr1c1, Ppar Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
symmetry	Space Group: P 41	R_factor 0.178 R_Free 0.239
crystal cell	length a length b length c angle alpha angle beta angle gamma 63.930 63.930 126.771 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.07 Å
ligand	NKS BindingDB	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	Discovery of an oxybenzylglycine based peroxisome proliferator activated receptor alpha selective agonist 2-((3-((2-(4-chlorophenyl)-5-methyloxazol-4-yl)methoxy)benzyl)(methoxycarb onyl)amino)acetic acid (BMS-687453)., Li J, Kennedy LJ, Shi Y, Tao S, Ye XY, Chen SY, Wang Y, Hernandez AS, Wang W, Devasthale PV, Chen S, Lai Z, Zhang H, Wu S, Smirk RA, Bolton SA, Ryono DE, Zhang H, Lim NK, Chen BC, Locke KT, O'Malley KM, Zhang L, Srivastava RA, Miao B, Meyers DS, Monshizadegan H, Search D, Grimm D, Zhang R, Harrity T, Kunselman LK, Cap M, Kadiyala P, Hosagrahara V, Zhang L, Xu C, Li YX, Muckelbauer JK, Chang C, An Y, Krystek SR, Blanar MA, Zahler R, Mukherjee R, Cheng PT, Tino JA, J Med Chem. 2010 Apr 8;53(7):2854-64. PMID:20218621

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk] Biological Unit Coordinates (3kdu.pdb1.gz) 95 Kb Biological Unit Coordinates (3kdu.pdb2.gz) 47 Kb Biological Unit Coordinates (3kdu.pdb3.gz) 50 Kb LPC: Ligand-Protein Contacts for 3KDU CSU: Contacts of Structural Units for 3KDU Structure Factors (495 Kb) Retrieve 3KDU in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3KDU from S2C, [Save to disk] Re-refined 3kdu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KDU 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 3KDU

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 3KDU, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3kdu_A] [3kdu_B] [3kdu] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3KDU: [HOLI ] by SMART

Other resources with information on 3KDU

Community annotation for 3KDU at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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