2Z94 | pdb_00002z94

Complex structure of SARS-CoV 3C-like protease with TDT

• PDB DOI: https://doi.org/10.2210/pdb2Z94/pdb

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


• Deposited: 2007-09-17 Released: 2007-12-25 
• Deposition Author(s): Lee, C.C., Wang, A.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors

Lee, C.C., Kuo, C.J., Hsu, M.F., Liang, P.H., Fang, J.M., Shie, J.J., Wang, A.H.

(2007) FEBS Lett 581: 5454-5458

• PubMed: 17981158 
• DOI: https://doi.org/10.1016/j.febslet.2007.10.048
• Primary Citation of Related Structures:  
  2Z94, 2Z9G, 2Z9J, 2Z9K, 2Z9L


• PubMed Abstract: 
  

  Five active metal-conjugated inhibitors (PMA, TDT, EPDTC, JMF1586 and JMF1600) bound with the 3C-like protease of severe acute respiratory syndrome (SARS)-associated coronavirus were analyzed crystallographically. The complex structures reveal two major inhibition modes: Hg(2+)-PMA is coordinated to C(44), M(49) and Y(54) with a square planar geometry at the S3 pocket, whereas each Zn(2+) of the four zinc-inhibitors is tetrahedrally coordinated to the H(41)-C(145) catalytic dyad. For anti-SARS drug design, this Zn(2+)-centered coordination pattern would serve as a starting platform for inhibitor optimization.

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Organizational Affiliation: 

Structural Biology Program, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.1 kDa 
• Atom Count: 2,834 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  EC: 3.4.22
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLD	C [auth A]	4-methylbenzene-1,2-dithiol C7 H8 S2 NIAAGQAEVGMHPM-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TLD	BindingDB:  2Z94	Ki: 1400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.511	α = 90
b = 81.548	β = 105.13
c = 53.334	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Lee, C.C., Wang, A.H.

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description