7KOL

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7KOL/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-09 Released: 2020-11-18 
• Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.206 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496

Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36.87 kDa 
• Atom Count: 2,527 
• Modelled Residue Count: 308 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease	A	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y96 (Subject of Investigation/LOI)	B [auth A]	5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide C21 H20 N2 O2 UTAGJMUNTWRPTE-IKMPRTQCSA-N
MES	K [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.206 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: I 4₁ 2 2
• Diffraction Data: https://doi.org/10.18430/m37kol

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.178	α = 90
b = 114.178	β = 90
c = 220.531	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2021-03-31
  Changes: Structure summary
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description