3D5E Hydrolase date May 16, 2008
title Crystal Structure Of Human Plasma Platelet Activating Factor Acetylhydrolase Covalently Inhibited By Paraoxon
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- Associated Phospholipase A2, Ldl-Pla(2), 2-Acetyl-1- Alkylglycerophosphocholine 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
R_factor 0.204 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
117.213 78.696 97.340 90.00 101.61 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand DEP, FMT enzyme Hydrolase E.C. BRENDA
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] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (3d5e.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3d5e.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 3D5E
  • CSU: Contacts of Structural Units for 3D5E
  • Likely Quarternary Molecular Structure file(s) for 3D5E
  • Structure Factors (1364 Kb)
  • Retrieve 3D5E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D5E from S2C, [Save to disk]
  • Re-refined 3d5e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D5E 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 3D5E
  • 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 3D5E, from MSDmotif at EBI
  • Fold representative 3d5e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d5e] [3d5e_A] [3d5e_B]
  • SWISS-PROT database: [Q13093]
  • Domain organization of [PAFA_HUMAN] by SWISSPFAM
  • Other resources with information on 3D5E
  • Community annotation for 3D5E 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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