5SSP

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166285 - (R,R) and (S,S) isomers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Ligand screen against SARS-CoV-2 NSP3 macrodomain

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D 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), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTU (Subject of Investigation/LOI)
Query on RTU

Download Ideal Coordinates CCD File 
D [auth A](1R,2R)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid
C19 H16 N2 O4
DEQJMLORKTWBPR-PBHICJAKSA-N
 Ligand Interaction
RTI (Subject of Investigation/LOI)
Query on RTI

Download Ideal Coordinates CCD File 
C [auth A](1S,2S)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid
C19 H16 N2 O4
DEQJMLORKTWBPR-WMLDXEAASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 
  • Space Group: P 43
  • Diffraction Data: https://doi.org/10.18430/M35SSP
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.693α = 90
b = 88.693β = 90
c = 39.334γ = 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 Foundation (NSF, United States)United States2031205

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release