5G3M Hydrolase date Apr 29, 2016
title Discovery Of A Novel Secreted Phospholipase A2 (Spla2) Inhib
authors J.Sandmark, C.Bodin, K.Hallberg
compound source
Molecule: Group 10 Secretory Phospholipase A2
Chain: A, B
Fragment: Mature Spla2-X, Unp Residues 43-165
Synonym: Secreted Phospholipase A2, Group X Secretory Phosp Spla2-X, Phosphatidylcholine 2-Acylhydrolase 10;
Ec: 3.1.1.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Gold
Expression_system_plasmid: Pet24a
symmetry Space Group: P 21 21 21
R_factor 0.199 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
27.570 85.122 103.316 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand 9JH, CA, DMS, PEG enzyme Hydrolase E.C.3.1.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • positive regulation of lipid...

  • Primary referenceDiscovery of AZD2716: A Novel Secreted Phospholipase A2 (sPLA2) Inhibitor for the Treatment of Coronary Artery Disease., Giordanetto F, Pettersen D, Starke I, Nordberg P, Dahlstrom M, Knerr L, Selmi N, Rosengren B, Larsson LO, Sandmark J, Castaldo M, Dekker N, Karlsson U, Hurt-Camejo E, ACS Med Chem Lett. 2016 Aug 9;7(10):884-889. eCollection 2016 Oct 13. PMID:27774123
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (5g3m.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (5g3m.pdb2.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 5G3M
  • CSU: Contacts of Structural Units for 5G3M
  • Structure Factors (387 Kb)
  • Retrieve 5G3M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5G3M from S2C, [Save to disk]
  • Re-refined 5g3m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5G3M in 3D
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  • Visual 3D analysis of 5G3M
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  • 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
  • Fold representative 5g3m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5g3m] [5g3m_A] [5g3m_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5G3M: [PA2c ] by SMART
  • Other resources with information on 5G3M
  • Community annotation for 5G3M at PDBWiki (http://pdbwiki.org)

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