5RT9

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000388280


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report



Literature

Fragment screen against SARS-CoV-2 NSP macrodomain

Correy, C.J.Fraser, J.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3AB169Severe 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 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
54G
Query on 54G

Download Ideal Coordinates CCD File 
A
2-hydroxy-5-methylbenzoic acid
C8 H8 O3
DLGBEGBHXSAQOC-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.742α = 90
b = 88.742β = 90
c = 39.392γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science FoundationUnited States2031205

Revision History 

  • Version 1.0: 2020-12-16
    Type: Initial release