5E6J Hydrolase date Oct 09, 2015
title Structure Of Sars Plpro Bound To A Lys48-Linked Di-Ubiquitin Based Probe
authors C.D.Lima, M.Bekes
compound source
Molecule: Replicase Polyprotein 1ab
Chain: A, D
Fragment: Unp Residues 1541-1856
Synonym: Pp1ab,Orf1ab Polyprotein
Ec: 3.4.19.12,3.4.22.69,3.4.22.-,2.7.7.48,3.6.4.12,3.6.4.13 3.1.13.-,3.1.-.-;
Engineered: Yes
Organism_scientific: Human Sars Coronavirus
Organism_common: Sars-Cov
Organism_taxid: 227859
Gene: Rep, 1a-1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21(De3) Ril Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: Ubiquitin
Chain: B, E
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 32630

Molecule: Polyubiquitin-B
Chain: C, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.232 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.981 68.239 119.021 90.00 103.21 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand 5MW, ACT, AYE, NI enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceRecognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease., Bekes M, van der Heden van Noort GJ, Ekkebus R, Ovaa H, Huang TT, Lima CD, Mol Cell. 2016 May 19;62(4):572-85. doi: 10.1016/j.molcel.2016.04.016. PMID:27203180
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (5e6j.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (5e6j.pdb2.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 5E6J
  • CSU: Contacts of Structural Units for 5E6J
  • Structure Factors (1282 Kb)
  • Retrieve 5E6J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E6J from S2C, [Save to disk]
  • Re-refined 5e6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E6J 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 5E6J
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e6j_B] [5e6j_E] [5e6j_D] [5e6j_A] [5e6j_F] [5e6j] [5e6j_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5E6J: [UBQ ] by SMART
  • Other resources with information on 5E6J
  • Community annotation for 5E6J at PDBWiki (http://pdbwiki.org)

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