7JN2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The crystal structure of Papain-Like Protease of SARS CoV-2 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Papain-like proteaseA318Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
L [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A], K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.76α = 90
b = 114.76β = 90
c = 217.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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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: 2020-08-12
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 2.0: 2021-02-03
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2021-03-31
    Changes: Structure summary