6Y2F Viral Protein date Feb 15, 2020
title Crystal Structure (Monoclinic Form) Of The Complex Resulting Reaction Between Sars-Cov-2 (2019-Ncov) Main Protease And T (1-((S)-1-(((S)-4-(Benzylamino)-3,4-Dioxo-1-((S)-2-Oxopyrro Yl)Butan-2-Yl)Amino)-3-Cyclopropyl-1-Oxopropan-2-Yl)-2-Oxo- Dihydropyridin-3-Yl)Carbamate (Alpha-Ketoamide 13b)
authors L.Zhang, D.Lin, X.Sun, R.Hilgenfeld
compound source
Molecule: 3c-Like Proteinase
Chain: A
Synonym: 3cl-Pro,3clp,Main Protease,Mpro,Non-Structural Pro Nsp5,Sars Coronavirus Main Proteinase;
Ec: 3.4.22.69
Engineered: Yes
Organism_scientific: Severe Acute Respiratory Syndrome Coro 2;
Organism_common: 2019-Ncov, Sars-Cov-2
Organism_taxid: 2697049
Gene: Rep, 1a-1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.178 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.085 80.926 51.659 90.00 114.84 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand DMS, O6K enzyme Hydrolase E.C.3.4.22.69 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (6y2f.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 6Y2F
  • CSU: Contacts of Structural Units for 6Y2F
  • Structure Factors (1108 Kb)
  • Retrieve 6Y2F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6Y2F from S2C, [Save to disk]
  • View 6Y2F 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 6Y2F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6y2f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6y2f_A] [6y2f_AAA]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6Y2F
  • Community annotation for 6Y2F at PDBWiki (http://pdbwiki.org)

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