7GZM

Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0008324-001

PDB DOI: https://doi.org/10.2210/pdb7GZM/pdb
Deposition Group: G_1002283 (changed state) ExploreG_1002283

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

Deposited: 2024-01-23 Released: 2024-05-15
Deposition Author(s): Aschenbrenner, J.C., Fearon, D., Tomlinson, C.W.E., Marples, P.G., Fairhead, M., Balcomb, B.H., Chandran, A.V., Godoy, A.S., Koekemoer, L., Lithgo, R.M., Ni, X., Thompson, W., Wang, S., Wild, C., Williams, E.P., Winokan, M., Walsh, M.A., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.210
R-Value Work: 0.189
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the ASAP AViDD centre

Aschenbrenner, J.C., Fearon, D., Tomlinson, C.W.E., Marples, P.G., Fairhead, M., Balcomb, B.H., Chandran, A.V., Godoy, A.S., Koekemoer, L., Lithgo, R.M., Ni, X., Thompson, W., Wang, S., Wild, C., Williams, E.P., Winokan, M., Walsh, M.A., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 36.59 kDa
Atom Count: 3,051
Modelled Residue Count: 333
Deposited Residue Count: 338
Unique protein chains: 1

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
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
A1AKT Query on A1AKT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	N-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-D-valine C₁₁ H₁₄ N₄ O₂ JDFXIEGECAJIPV-MRVPVSSYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.210
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.126	α = 90
b = 89.126	β = 90
c = 39.544	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Aschenbrenner, J.C.

Tomlinson, C.W.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171399

Revision History (Full details and data files)

Version 1.0: 2024-05-15
Type: Initial release

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 R01GM133198.