7XAX

Crystal structure of SARS coronavirus main protease in complex with Baicalei

PDB DOI: https://doi.org/10.2210/pdb7XAX/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome-related coronavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-03-19 Released: 2023-03-22
Deposition Author(s): Zhou, X.L., Li, J., Zhang, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.280
R-Value Work: 0.229
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of SARS coronavirus main protease in complex with Baicalei

Zhou, X.L., Li, J., Zhang, J.

To be published.

Macromolecule Content

Total Structure Weight: 68.02 kDa
Atom Count: 4,435
Modelled Residue Count: 594
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 EC: 3.4.22.69
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3WL (Subject of Investigation/LOI) Query on 3WL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one C₁₅ H₁₀ O₅ FXNFHKRTJBSTCS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.280
R-Value Work: 0.229
R-Value Observed: 0.232
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.51	α = 90.951
b = 60.55	β = 102.715
c = 68.28	γ = 108.649

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.