8GQT | pdb_00008gqt

Structure of Mpro complexed with Quercetin

PDB DOI: https://doi.org/10.2210/pdb8GQT/pdb

Classification: CELL INVASION
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-08-30 Released: 2023-08-30
Deposition Author(s): Dong, J., Yang, G.-F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.253 (Depositor), 0.291 (DCC)
R-Value Work:
0.205 (Depositor)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of Mpro complexed with Quercetin

Dong, J., Yang, G.-F.

To be published.

Macromolecule Content

Total Structure Weight: 33.75 kDa
Atom Count: 2,404
Modeled Residue Count: 299
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth D]	303	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.22.69
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
QUE (Subject of Investigation/LOI) Query on QUE Download:Ideal Coordinates CCD File SDF format, chain B [auth D] MOL2 format, chain B [auth D] mmCIF format, chain B [auth D]	B [auth D]	3,5,7,3',4'-PENTAHYDROXYFLAVONE C₁₅ H₁₀ O₇ REFJWTPEDVJJIY-UHFFFAOYSA-N		Interactions Focus chain B [auth D] Interactions & Density Focus chain B [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.253 (Depositor), 0.291 (DCC)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.304	α = 90
b = 81.715	β = 114.69
c = 51.594	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, 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.