5KRE Hydrolase Hydrolase Inhibitor date Jul 07, 2016
title Covalent Inhibitor Of Lyplal1
authors J.Pandit
compound source
Molecule: Lysophospholipase-Like Protein 1
Chain: A
Ec: 3.1.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lyplal1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.410 61.440 75.980 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 6WG, NO3 enzyme Hydrolase E.C.3.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiscovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism., Ahn K, Boehm M, Brown MF, Calloway J, Che Y, Chen J, Fennell KF, Geoghegan KF, Gilbert AM, Gutierrez JA, Kalgutkar AS, Lanba A, Limberakis C, Magee TV, O'Doherty I, Oliver R, Pabst B, Pandit J, Parris K, Pfefferkorn JA, Rolph TP, Patel R, Schuff B, Shanmugasundaram V, Starr JT, Varghese AH, Vera NB, Vernochet C, Yan J, ACS Chem Biol. 2016 Jul 19. PMID:27391855
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (5kre.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 5KRE
  • CSU: Contacts of Structural Units for 5KRE
  • Structure Factors (430 Kb)
  • Retrieve 5KRE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KRE from S2C, [Save to disk]
  • Re-refined 5kre structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KRE 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 5KRE
  • 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
  • Fold representative 5kre from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kre_A] [5kre]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KRE
  • Community annotation for 5KRE at PDBWiki (http://pdbwiki.org)

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