6VXS Viral Protein date Feb 24, 2020
title Crystal Structure Of Adp Ribose Phosphatase Of Nsp3 From Sar
authors Y.Kim, R.Jedrzejczak, N.Maltseva, M.Endres, A.Mesecar, K.Michalsk A.Joachimiak, Center For Structural Genomics Of Infectious D (Csgid)
compound source
Molecule: Non-Structural Protein 3
Chain: A, B
Synonym: Nsp3,Adp Ribose Phosphatase,Pl2-Pro,Papain-Like Pr Papain-Like Proteinase,Pl-Pro;
Ec: 3.4.19.121, 3.4.22.-
Engineered: Yes
Organism_scientific: Severe Acute Respiratory Syndrome Coro 2;
Organism_common: 2019-Ncov
Organism_taxid: 2697049
Gene: Rep, 1a-1b
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 1
R_factor 0.186 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
30.391 37.896 65.400 84.37 82.11 90.11
method X-Ray Diffractionresolution 2.03 Å
ligand EDO, NHE, SO4 enzyme Hydrolase E.C.3.4.19.121 BRENDA
Primary referenceCrystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes., Michalska K, Kim Y, Jedrzejczak R, Maltseva NI, Stols L, Endres M, Joachimiak A, IUCrJ. 2020 Jul 17;7(Pt 5):814-824. doi: 10.1107/S2052252520009653. eCollection, 2020 Sep 1. PMID:32939273
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (6vxs.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (6vxs.pdb2.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 6VXS
  • CSU: Contacts of Structural Units for 6VXS
  • Structure Factors (564 Kb)
  • Retrieve 6VXS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VXS from S2C, [Save to disk]
  • View 6VXS 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 6VXS
  • 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 6vxs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vxs_B] [6vxs_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VXS
  • Community annotation for 6VXS at PDBWiki (http://pdbwiki.org)

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