3D59 Hydrolase date May 16, 2008
title Crystal Structure Of Human Plasma Platelet Activating Factor Acetylhydrolase
authors U.Samanta, B.J.Bahnson
compound source
Molecule: Platelet-Activating Factor Acetylhydrolase
Chain: A, B
Fragment: Unp Residues 47-429
Synonym: Paf Acetylhydrolase, Paf 2-Acylhydrolase, Ldl-Asso Phospholipase A2, Ldl-Pla(2), 2-Acetyl-1-Alkylglycerophosph Esterase, 1-Alkyl-2-Acetylglycerophosphocholine Esterase;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pla2g7, Pafah
Expression_system: Escherichia Coli
Expression_system_vector_type: Plasmid
symmetry Space Group: C 1 2 1
length a length b length c angle alpha angle beta angle gamma
116.184 83.061 96.705 90.00 115.09 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand ACT, SO4 enzyme Hydrolase E.C. BRENDA
note 3D59 is a representative structure
A, B

Primary referenceCrystal Structure of Human Plasma Platelet-activating Factor Acetylhydrolase: STRUCTURAL IMPLICATION TO LIPOPROTEIN BINDING AND CATALYSIS., Samanta U, Bahnson BJ, J Biol Chem. 2008 Nov 14;283(46):31617-24. Epub 2008 Sep 10. PMID:18784071
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (272 Kb) [Save to disk]
  • Biological Unit Coordinates (3d59.pdb1.gz) 137 Kb
  • Biological Unit Coordinates (3d59.pdb2.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 3D59
  • CSU: Contacts of Structural Units for 3D59
  • Likely Quarternary Molecular Structure file(s) for 3D59
  • Structure Factors (1127 Kb)
  • Retrieve 3D59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D59 from S2C, [Save to disk]
  • Re-refined 3d59 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D59 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 3D59
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3D59, from MSDmotif at EBI
  • Fold representative 3d59 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d59_A] [3d59] [3d59_B]
  • SWISS-PROT database: [Q13093]
  • Domain organization of [PAFA_HUMAN] by SWISSPFAM
  • Other resources with information on 3D59
  • Community annotation for 3D59 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
    Bioinformatics Unit
    Weizmann Institute of Science