Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69.62 kDa 
• Atom Count: 4875 
• Residue Count: 618 
• Unique protein chains: 2

1UK4

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor

• DOI: 10.2210/pdb1UK4/pdb

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


• Deposited: 2003-08-14 Released: 2003-11-18 
• Deposition Author(s): Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.213 
• R-Value Observed: 0.229 

Literature

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor

Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G.F., Anand, K., Bartlam, M., Hilgenfeld, R., Rao, Z.

(2003) Proc Natl Acad Sci U S A 100: 13190-13195

• PubMed: 14585926 
• DOI: 10.1073/pnas.1835675100
• Primary Citation of Related Structures:  
  1UJ1, 1UK4, 1UK3, 1UK2


• PubMed Abstract: 
  

A newly identified severe acute respiratory syndrome coronavirus (SARS-CoV), is the etiological agent responsible for the outbreak of SARS. The SARS-CoV main protease, which is a 33.8-kDa protease (also called the 3C-like protease), plays a pivotal role in mediating viral replication and transcription functions through extensive proteolytic processing of two replicase polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Here, we report the crystal structures of the SARS-CoV main protease at different pH values and in complex with a specific inhibitor. The protease structure has a fold that can be described as an augmented serine-protease, but with a Cys-His at the active site. This series of crystal structures, which is the first, to our knowledge, of any protein from the SARS virus, reveal substantial pH-dependent conformational changes, and an unexpected mode of inhibitor binding, providing a structural basis for rational drug design.

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Organizational Affiliation: 

Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, 100084 Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.24 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-mer peptide of inhibitor	G, H, K	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATO	A, B	CHLOROACETONE C3 H5 Cl O BULLHNJGPPOUOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.213 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.633	α = 90
b = 97.735	β = 102.79
c = 67.931	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-14 
• Released Date: 2003-11-18 
Deposition Author(s): Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z.

Revision History 

• Version 1.0: 2003-11-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance