7KRX

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6WRH


Literature

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease318Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y41 (Subject of Investigation/LOI)
Query on Y41

Download Ideal Coordinates CCD File 
B [auth A]3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
C20 H20 N2 O
PZEBTCMUWPLVEX-CQSZACIVSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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I [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX
Query on UNX

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.333α = 90
b = 114.333β = 90
c = 219.573γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    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