Macromolecule Content

Total Structure Weight: 36.79 kDa
Atom Count: 3,589
Modelled Residue Count: 336
Deposited Residue Count: 338
Unique protein chains: 1

5SRD

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5373433723 - (S) isomer

PDB DOI: https://doi.org/10.2210/pdb5SRD/pdb
Deposition Group: G_1002239 (changed state) ExploreG_1002239

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

Deposited: 2022-06-09 Released: 2022-07-06
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: 0.165
R-Value Work: 0.147
R-Value Observed: 0.148

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
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 (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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R8K (Subject of Investigation/LOI) Query on R8K Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(8S)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-N-(methanesulfonyl)-6-azaspiro[3.4]octane-8-carboxamide C₁₉ H₁₉ F₂ N₅ O₃ S KZZPVTBGUAEVQI-IBGZPJMESA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.165
R-Value Work: 0.147
R-Value Observed: 0.148
Space Group: P 4₃
Diffraction Data: https://doi.org/10.18430/M35SRD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.75	α = 90
b = 88.75	β = 90
c = 39.565	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

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: 2022-07-06
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.