5YIK Transferase Protein Binding date Oct 05, 2017
title Structure Of A Legionella Effector With Its Substrate
authors Y.Feng, Y.Dong, Z.Liu
compound source
Molecule: Sdea
Chain: A
Fragment: Unp Residues 236-1195
Engineered: Yes
 Organism_scientific: Legionella Pneumophila
Organism_taxid: 446
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin
Chain: C, D, F
Fragment: Unp Residues 1-76
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.223 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.846 145.893 104.088 90.00 104.46 90.00
method X-Ray Diffractionresolution 3.10 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of ubiquitin modification by the Legionella effector SdeA., Dong Y, Mu Y, Xie Y, Zhang Y, Han Y, Zhou Y, Wang W, Liu Z, Wu M, Wang H, Pan M, Xu N, Xu CQ, Yang M, Fan S, Deng H, Tan T, Liu X, Liu L, Li J, Wang J, Fang X, Feng Y, Nature. 2018 May;557(7707):674-678. doi: 10.1038/s41586-018-0146-7. Epub 2018 May, 23. PMID:29795342
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (195 Kb) [Save to disk]
  • Biological Unit Coordinates (5yik.pdb1.gz) 191 Kb
  • CSU: Contacts of Structural Units for 5YIK
  • Structure Factors (750 Kb)
  • Retrieve 5YIK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YIK from S2C, [Save to disk]
    • View 5YIK 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 5YIK
  • 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: [5yik_A] [5yik_C] [5yik_D] [5yik_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5YIK
  • Community annotation for 5YIK at PDBWiki (http://pdbwiki.org)

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