3DY5	Lyase, Oxidoreductase	date	Jul 25, 2008
title	Allene Oxide Synthase 8r-Lipoxygenase From Plexaura Homomall
authors	N.C.Gilbert, M.Niebuhr, H.Tsuruta, M.E.Newcomer
compound		source
Molecule: Allene Oxide Synthase-Lipoxygenase Protein Chain: A, C Synonym: [Includes: Allene Oxide Synthase (Ec 4.2.1.92) (Hydroperoxidehydrase), And Arachidonate 8-Lipoxygenase (Ec 1.13.11.40)]; Ec: 4.2.1.92, 1.13.11.40 Engineered: Yes		Organism_scientific: Plexaura Homomalla Organism_common: Black Sea Rod Organism_taxid: 47982 Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptbfusion
symmetry	Space Group: C 1 2 1	R_factor 0.273 R_Free 0.322
crystal cell	length a length b length c angle alpha angle beta angle gamma 235.520 77.493 157.966 90.00 112.45 90.00
method	X-Ray Diffraction	resolution	3.51 Å
ligand	FE2, HEM	enzyme	Lyase E.C.4.2.1.92 BRENDA
Gene Ontology	Chain Function Process Component A, C catalase activity
Primary reference	A covalent linker allows for membrane targeting of an oxylipin biosynthetic complex., Gilbert NC, Niebuhr M, Tsuruta H, Bordelon T, Ridderbusch O, Dassey A, Brash AR, Bartlett SG, Newcomer ME, Biochemistry. 2008 Oct 7;47(40):10665-76. Epub 2008 Sep 12. PMID:18785758

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (282 Kb) [Save to disk] Biological Unit Coordinates (3dy5.pdb1.gz) 138 Kb Biological Unit Coordinates (3dy5.pdb2.gz) 139 Kb LPC: Ligand-Protein Contacts for 3DY5 CSU: Contacts of Structural Units for 3DY5 Likely Quarternary Molecular Structure file(s) for 3DY5 Structure Factors (532 Kb) Retrieve 3DY5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DY5 from S2C, [Save to disk] Re-refined 3dy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DY5 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 3DY5

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 3DY5, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dy5_C] [3dy5_A] [3dy5] SWISS-PROT database: [O16025] Domain organization of [AOSL_PLEHO] by SWISSPFAM Domain found in 3DY5: [LH2 ] by SMART

Other resources with information on 3DY5

Community annotation for 3DY5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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