3O0D Hydrolase date Jul 19, 2010
title Crystal Structure Of Lip2 Lipase From Yarrowia Lipolytica At Resolution
authors F.Bordes, S.Tranier, L.Mourey, A.Marty
compound source
Molecule: Triacylglycerol Lipase
Chain: A, B, C, D, E, F, G
Synonym: Yali0a20350p
Ec: 3.1.1.3
Engineered: Yes
 Organism_scientific: Yarrowia Lipolytica
Organism_common: Candida Lipolytica
Organism_taxid: 4952
Gene: Lip2, Yali0a20350g
Expression_system: Yarrowia Lipolytica
Expression_system_taxid: 4952
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.354 132.141 137.255 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand K, MPD, MRD, NAG enzyme Hydrolase E.C.3.1.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, G, E, B


Primary referenceExploring the conformational states and rearrangements of Yarrowia lipolytica Lipase., Bordes F, Barbe S, Escalier P, Mourey L, Andre I, Marty A, Tranier S, Biophys J. 2010 Oct 6;99(7):2225-34. PMID:20923657
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (377 Kb) [Save to disk]
  • Biological Unit Coordinates (3o0d.pdb1.gz) 59 Kb
  • Biological Unit Coordinates (3o0d.pdb2.gz) 59 Kb
  • Biological Unit Coordinates (3o0d.pdb3.gz) 58 Kb
  • Biological Unit Coordinates (3o0d.pdb4.gz) 56 Kb
  • Biological Unit Coordinates (3o0d.pdb5.gz) 59 Kb
  • Biological Unit Coordinates (3o0d.pdb6.gz) 57 Kb
  • Biological Unit Coordinates (3o0d.pdb7.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3O0D
  • CSU: Contacts of Structural Units for 3O0D
  • Structure Factors (3419 Kb)
  • Retrieve 3O0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O0D from S2C, [Save to disk]
  • Re-refined 3o0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3O0D 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 3O0D
  • 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 3O0D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o0d_E] [3o0d_C] [3o0d] [3o0d_B] [3o0d_F] [3o0d_G] [3o0d_D] [3o0d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3O0D
  • Community annotation for 3O0D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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