5JAU Hydrolase date Apr 12, 2016
title Exploitation Of A Novel Binding Pocket In Human Lipoprotein- Phospholipase A2 (Lp-Pla2) Discovered Through X- Fragment Screening
authors P.J.Day
compound source
Molecule: Platelet-Activating Factor Acetylhydrolase
Chain: A
Synonym: Paf Acetylhydrolase,1-Alkyl-2-Acetylglycerophospho Esterase,2-Acetyl-1-Alkylglycerophosphocholine Esterase,Gro Phospholipase A2,Gviia-Pla2,Ldl-Associated Phospholipase A2 Pla(2),Paf 2-Acylhydrolase;
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
symmetry Space Group: C 1 2 1
R_factor 0.202 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.783 90.533 51.499 90.00 111.83 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand 6HU, CL, DMS enzyme Hydrolase E.C.3.1.1.47 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceExploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA) Discovered through X-ray Fragment Screening., Woolford AJ, Pero JE, Aravapalli S, Berdini V, Coyle JE, Day PJ, Dodson AM, Grondin P, Holding FP, Lee LY, Li P, Manas ES, Marino J Jr, Martin AC, McCleland BW, McMenamin RL, Murray CW, Neipp CE, Page LW, Patel VK, Potvain F, Rich S, Rivero RA, Smith K, Somers DO, Trottet L, Velagaleti R, Williams G, Xie R, J Med Chem. 2016 May 20. PMID:27167608
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (5jau.pdb1.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 5JAU
  • CSU: Contacts of Structural Units for 5JAU
  • Structure Factors (792 Kb)
  • Retrieve 5JAU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JAU from S2C, [Save to disk]
  • Re-refined 5jau structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JAU 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 5JAU
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jau] [5jau_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5JAU
  • Community annotation for 5JAU at PDBWiki (http://pdbwiki.org)

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