5RUQ

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000032199226


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Fragment screen against SARS-CoV-2 NSP macrodomain

Correy, G.J.Fraser, J.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3A, B169Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 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)
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W6D (Subject of Investigation/LOI)
Query on W6D

Download Ideal Coordinates CCD File 
C [auth A]1H-indole-4-carboxamide
C9 H8 N2 O
ACRGIRLCXXEJCS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 43
  • Diffraction Data DOI: 10.18430/m35ruq Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.718α = 90
b = 88.718β = 90
c = 39.473γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science FoundationUnited States2031205

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 1.2: 2021-05-12
    Changes: Structure summary
  • Version 1.3: 2021-06-09
    Changes: Structure summary