6XB2 Viral Protein, Hydrolase date Jun 05, 2020
title Room Temperature X-Ray Crystallography Reveals Catalytic Cys The Sars-Cov-2 3cl Mpro Is Highly Reactive: Insights For En Mechanism And Drug Design
authors D.W.Kneller, A.Kovalevsky, L.Coates
compound source
Molecule: 3c-Like Proteinase
Chain: A
Synonym: 3cl-Pro, 3clp
Ec: 3.4.22.69
Engineered: Yes
 Organism_scientific: Severe Acute Respiratory Syndrome Coro 2;
Organism_common: 2019-Ncov
Organism_taxid: 2697049
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 1 2 1
R_factor 0.196 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.292 54.636 115.157 90.00 100.74 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand DMS, NEN enzyme Hydrolase E.C.3.4.22.69 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRoom-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M(pro): insights into enzyme mechanism and drug design., Kneller DW, Phillips G, O'Neill HM, Tan K, Joachimiak A, Coates L, Kovalevsky A, IUCrJ. 2020 Sep 21;7(Pt 6). pii: S2052252520012634. doi:, 10.1107/S2052252520012634. PMID:33063790
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (6xb2.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 6XB2
  • CSU: Contacts of Structural Units for 6XB2
  • Structure Factors (682 Kb)
  • Retrieve 6XB2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6XB2 from S2C, [Save to disk]
    • View 6XB2 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 6XB2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m6xb2, region B:136-422 [Jmol] [rasmolscript] [script source]
        - Domain d1t6xb2, region B:302-458 [Jmol] [rasmolscript] [script source]
        - Domain d1q6xb2, region B:402-617 [Jmol] [rasmolscript] [script source]
        - Domain d1v6xb2, region B:501-803 [Jmol] [rasmolscript] [script source]
        - Domain d1i6xb2, region B:8-137 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6xb2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6XB2
  • Community annotation for 6XB2 at PDBWiki (http://pdbwiki.org)

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