Macromolecule Content

Total Structure Weight: 36.55 kDa
Atom Count: 3092
Residue Count: 336
Unique protein chains: 1

5RUN

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000194295

DOI: 10.2210/pdb5RUN/pdb
Deposition Group: G_1002171 ()

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

Deposited: 2020-09-28 Released: 2020-12-16
Deposition Author(s): Correy, G.J., Young, I.D., Thompson, M.C., Fraser, J.S.
Funding Organization(s): National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.171
R-Value Work: 0.159
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

This is version 1.1 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
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), 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EXB Query on EXB Download Ideal Coordinates CCD File SDF format, chain C [A] MOL2 format, chain C [A]	A	3-(1H-benzimidazol-1-yl)propanoic acid C₁₀ H₁₀ N₂ O₂ XKGRXBQGCQJOHQ-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.171
R-Value Work: 0.159
R-Value Observed: 0.159
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.718	α = 90
b = 88.718	β = 90
c = 39.466	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

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-09-28
Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation	United States	2031205

Revision History

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2021-01-27
Changes: Structure summary

RCSB PDB is 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.