6YWL

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose

Schroeder, M.Ni, X.Olieric, V.Sharpe, E.M.Wojdyla, J.A.Wang, M.Knapp, S.Chaikuad, A.Structural Genomics Consortium (SGC)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NSP3 macrodomain
A, B, C, D, E
173Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTD1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download CCD File 
A, B, C, D, E
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D, E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.395α = 90
b = 111.922β = 90
c = 195.333γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-06
    Type: Initial release