3F98 Hydrolase date Nov 13, 2008
title Crystal Structure Of Human Plasma Platelet Activating Factor Acetylhydrolase Covalently Inhibited By Tabun
authors U.Samanta, B.J.Bahnson
compound source
Molecule: Platelet-Activating Factor Acetylhydrolase
Chain: A, B, C
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;
Ec: 3.1.1.47
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pla2g7, Pafah
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: C 2 2 21
R_factor 0.179 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.984 133.322 253.855 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand FMT, NTJ enzyme Hydrolase E.C.3.1.1.47 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes., Samanta U, Kirby SD, Srinivasan P, Cerasoli DM, Bahnson BJ, Biochem Pharmacol. 2009 Aug 15;78(4):420-9. Epub 2009 Apr 24. PMID:19394314
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (226 Kb) [Save to disk]
  • Biological Unit Coordinates (3f98.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (3f98.pdb2.gz) 77 Kb
  • Biological Unit Coordinates (3f98.pdb3.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 3F98
  • CSU: Contacts of Structural Units for 3F98
  • Likely Quarternary Molecular Structure file(s) for 3F98
  • Structure Factors (3446 Kb)
  • Retrieve 3F98 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F98 from S2C, [Save to disk]
  • Re-refined 3f98 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F98 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 3F98
  • 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 3F98, from MSDmotif at EBI
  • Fold representative 3f98 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f98_A] [3f98] [3f98_C] [3f98_B]
  • SWISS-PROT database: [Q13093]
  • Domain organization of [PAFA_HUMAN] by SWISSPFAM
  • Other resources with information on 3F98
  • Community annotation for 3F98 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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