9RHO | pdb_00009rho

Structure of SARS-coV-2 NSP3 macrodomain in complex with ligand

PDB DOI: https://doi.org/10.2210/pdb9RHO/pdb

Classification: VIRUS
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-09 Released: 2026-06-24
Deposition Author(s): Ruiz Carrillo, D., Sander, S., Tidow, H., Garcia-Alai, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.142 (Depositor), 0.192 (DCC)
R-Value Work:
0.125 (Depositor), 0.162 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Model: experimental
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Literature

Targeting a viral macrodomain: Design, structure-based optimization and antiviral evaluation of potent inhibitors for Mac1 of SARS-CoV-2

Fliegert, R., Sandmann, M., Tajdar, S., Sander, S., Carrillo, D., Ganter, B., Ocenas, M., Etzold, S., Pekarek, N., Berger, J., Meister, T.L., Watt, J., Baszczynski, O., Potter, B., Alai, M.G., Henning, T., Susanne, P., Meier, C.

To be published.

Macromolecule Content

Total Structure Weight: 37.37 kDa
Atom Count: 3,005
Modeled Residue Count: 338
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JGA (Subject of Investigation/LOI) Query on A1JGA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] methyl hydrogen phosphate C₁₃ H₁₇ N₅ O₁₀ P₂ LHSHZBZZZUSBLE-VUXODMRMSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.142 (Depositor), 0.192 (DCC)
R-Value Work: 0.125 (Depositor), 0.162 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.8	α = 90
b = 82.8	β = 90
c = 41.27	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Ruiz Carrillo, D.

Garcia-Alai, M.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1328

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release
Version 1.1: 2026-07-01
Changes: Database references

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