8CB3 | pdb_00008cb3

SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid

PDB DOI: https://doi.org/10.2210/pdb8CB3/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-01-25 Released: 2024-02-07
Deposition Author(s): Morin, B., Ferron, F., Coutard, B., Canard, B., Marseilles Structural Genomics Program @ AFMB (MSGP)
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.203 (Depositor), 0.201 (DCC)
R-Value Work:
0.179 (Depositor), 0.176 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Derivatives of MOPS: Promising scaffolds for SARS Coronaviruses macro domain-targeted inhibition

Ortega-Granda, O., Morin, B., Alvarez, K., Feracci, M., Coutard, B., Canard, B., Ferron, F., Rabah, N.

(2025) FEBS J

DOI: https://doi.org/10.1111/febs.70039

Macromolecule Content

Total Structure Weight: 56.21 kDa
Atom Count: 4,464
Modeled Residue Count: 517
Deposited Residue Count: 522
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, C	174	Severe acute respiratory syndrome coronavirus	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPO (Subject of Investigation/LOI) Query on MPO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.203 (Depositor), 0.201 (DCC)
R-Value Work: 0.179 (Depositor), 0.176 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.285	α = 90
b = 55.405	β = 91.7
c = 108.671	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Marseilles Structural Genomics Program @ AFMB (MSGP)

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	VIZIER Grant agreement ID: 511960

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release
Version 1.1: 2025-02-26
Changes: Database references, Structure summary

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.