1P9S

Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs

• PDB DOI: https://doi.org/10.2210/pdb1P9S/pdb

• Classification: HYDROLASE
• Organism(s): Human coronavirus 229E
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-12 Released: 2003-05-20 
• Deposition Author(s): Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J.R., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.279 
• R-Value Work: 0.196 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs

Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J.R., Hilgenfeld, R.

(2003) Science 300: 1763-1767

• PubMed: 12746549 
• DOI: https://doi.org/10.1126/science.1085658
• Primary Citation of Related Structures:  
  1P9S, 1P9U


• PubMed Abstract: 
  

  A novel coronavirus has been identified as the causative agent of severe acute respiratory syndrome (SARS). The viral main proteinase (Mpro, also called 3CLpro), which controls the activities of the coronavirus replication complex, is an attractive target for therapy. We determined crystal structures for human coronavirus (strain 229E) Mpro and for an inhibitor complex of porcine coronavirus [transmissible gastroenteritis virus (TGEV)] Mpro, and we constructed a homology model for SARS coronavirus (SARS-CoV) Mpro. The structures reveal a remarkable degree of conservation of the substrate-binding sites, which is further supported by recombinant SARS-CoV Mpro-mediated cleavage of a TGEV Mpro substrate. Molecular modeling suggests that available rhinovirus 3Cpro inhibitors may be modified to make them useful for treating SARS.

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Organizational Affiliation: 

Institute of Biochemistry, University of Lübeck, D-23538 Lübeck, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.8 kDa 
• Atom Count: 4,633 
• Modelled Residue Count: 599 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B	300	Human coronavirus 229E	Mutation(s): 10  Gene Names: ORF1a EC: 3.4.24
UniProt
Find proteins for P0C6U2 (Human coronavirus 229E) Explore P0C6U2  Go to UniProtKB:  P0C6U2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	C [auth A], D [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.279 
• R-Value Work: 0.196 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.356	α = 90
b = 76.24	β = 103.7
c = 73.477	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-20 
Deposition Author(s): Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J.R., Hilgenfeld, R.

Revision History  

• Version 1.0: 2003-05-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-10-30
  Changes: Structure summary