5ZKQ Signaling Protein date Mar 25, 2018
title Crystal Structure Of The Human Platelet-Activating Factor Re Complex With Abt-491
authors C.Cao, Q.Zhao, X.C.Zhang, B.Wu
compound source
Molecule: Platelet-Activating Factor Receptor,Endolysin,End Platelet-Activating Factor Receptor;
Chain: A, B
Synonym: Pafr, Lysis Protein, Lysozyme, Muramidase
Ec: 3.2.1.17
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens, Enterobacteria Phage T4
Organism_common: Human, Bacteriophage T4
Organism_taxid: 9606, 10665
Gene: Ptafr, Pafr
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: C 1 2 1
R_factor 0.203 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.220 166.540 100.310 90.00 100.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 9EU, OLC, SO4, ZN enzyme Hydrolase E.C.3.2.1.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for signal recognition and transduction by platelet-activating-factor receptor., Cao C, Tan Q, Xu C, He L, Yang L, Zhou Y, Zhou Y, Qiao A, Lu M, Yi C, Han GW, Wang X, Li X, Yang H, Rao Z, Jiang H, Zhao Y, Liu J, Stevens RC, Zhao Q, Zhang XC, Wu B, Nat Struct Mol Biol. 2018 Jun;25(6):488-495. doi: 10.1038/s41594-018-0068-y. Epub, 2018 May 28. PMID:29808000
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (120 Kb) [Save to disk]
  • Biological Unit Coordinates (5zkq.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 5ZKQ
  • CSU: Contacts of Structural Units for 5ZKQ
  • Structure Factors (1110 Kb)
  • Retrieve 5ZKQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZKQ from S2C, [Save to disk]
    • View 5ZKQ 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 5ZKQ
  • 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: [5zkq_B] [5zkq_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5ZKQ
  • Community annotation for 5ZKQ at PDBWiki (http://pdbwiki.org)

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