9GHN | pdb_00009ghn

Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of Q256A

PDB DOI: https://doi.org/10.2210/pdb9GHN/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-15 Released: 2025-09-03
Deposition Author(s): Creon, A., Scheer, T.E.S., Lane, T.J., Rahmani Mashhour, A., Guenther, S., Reinke, P.Y.A., Meents, A., Chapman, H.N.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.218 (Depositor), 0.195 (DCC)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of Q256A

Creon, A., Scheer, T.E.S., Lane, T.J., Rahmani Mashhour, A., Guenther, S., Reinke, P.Y.A., Meents, A., Chapman, H.N.

To be published.

Macromolecule Content

Total Structure Weight: 67.84 kDa
Atom Count: 5,537
Modeled Residue Count: 612
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 EC: 3.4.22.69
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.218 (Depositor), 0.195 (DCC)
R-Value Work: 0.193 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.538	α = 90
b = 88.438	β = 90
c = 100.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Rahmani Mashhour, A.

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release

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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.