8YSA | pdb_00008ysa

The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H102

PDB DOI: https://doi.org/10.2210/pdb8YSA/pdb

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

Deposited: 2024-03-22 Released: 2024-05-08
Deposition Author(s): Zheng, W.Y., Fu, L.F., Feng, Y., Han, P., Qi, J.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.197 (Depositor), 0.192 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YSA

This is version 1.0 of the entry. See complete history.

Literature

Discovery, Biological Activity, and Structural Mechanism of a Potent Inhibitor of SARS-CoV-2 Main Protease

Wang, J., Sang, X.H., Zheng, W.Y., Chan, J.F., Zhou, J., Xu, Y., Fu, L.F., Feng, Y., Han, P., Tsang, J.O., Yuan, S.F., An, J., Yuen, K.Y., Qi, J.X., Huang, Z.W.

To be published.

Macromolecule Content

Total Structure Weight: 34.34 kDa
Atom Count: 2,689
Modeled Residue Count: 308
Deposited Residue Count: 310
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BOC-TBG-PHE-ELL	B	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TBG Query on TBG	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.197 (Depositor), 0.192 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.334	α = 90
b = 106.334	β = 90
c = 82.17	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
Coot	model building
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-05-08
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.