14AM | pdb_000014am

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8207599372

PDB DOI: https://doi.org/10.2210/pdb14AM/pdb
Deposition Group: G_1002370 (changed state) | Explore G_1002370

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

Deposited: 2026-03-25 Released: 2026-09-16
Deposition Author(s): Correy, G.J., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free:
0.165 (Depositor), 0.171 (DCC)
R-Value Work:
0.147 (Depositor), 0.157 (DCC)
R-Value Observed:
0.148 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Development of a random background to understand ligand optimization

Xu, X., Mailhot, O., Correy, G.J., Huang, X.P., Braz, J., Shi, D., Srinivasan, K., Zielinski, K., Holota, Y., Kuziv, Y., Tsoutsouvas, C., Levinzon, N., Doruk, Y.U., Rachman, M., Diolaiti, M., Stevens, M., Liu, F., Holland, K., Hubner, H., Wang, J., Wu, Y., Ashworth, A., Makriyannis, A., Zhang, Y., Moroz, Y., Gmeiner, P., Abel, R., Manglik, A., Basbaum, A.I., Roth, B.L., Fraser, J.S., Shoichet, B.K.

(2026) Nature

DOI: https://doi.org/10.1038/s41586-026-11013-5

Macromolecule Content

Total Structure Weight: 36.72 kDa
Atom Count: 3,644
Modeled Residue Count: 336
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1DBL Query on A1DBL 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]	5-chloro-N-[(1S)-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methylpropyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine C₁₈ H₁₉ Cl N₄ O₂ POALVXMAIPIXGH-INIZCTEOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free: 0.165 (Depositor), 0.171 (DCC)
R-Value Work: 0.147 (Depositor), 0.157 (DCC)
R-Value Observed: 0.148 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.707	α = 90
b = 88.707	β = 90
c = 39.452	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110
National Institutes of Health/Office of the Director	United States	AY1AX000035

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release
Version 1.1: 2026-09-23
Changes: Database references