8ERS

PanDDA analysis -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398507 - (R,S) isomer

PDB DOI: https://doi.org/10.2210/pdb8ERS/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-12 Released: 2022-11-09
Deposition Author(s): Correy, G.J., Fraser, J.S.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.162
R-Value Work: 0.142
R-Value Observed: 0.143

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Ligand screen against SARS-CoV-2 NSP3 macrodomain

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

To be published.

Macromolecule Content

Total Structure Weight: 36.67 kDa
Atom Count: 3,973
Modelled Residue Count: 336
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WQO (Subject of Investigation/LOI) Query on WQO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1R,2S)-1-[(4-amino-2-hydroxybenzoyl)oxy]-2,3-dihydro-1H-indene-2-carboxylic acid C₁₇ H₁₅ N O₅ DWGIEIVAFVJIQU-ZFWWWQNUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.162
R-Value Work: 0.142
R-Value Observed: 0.143
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.812	α = 90
b = 88.812	β = 90
c = 39.325	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2031205

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.