7M1Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

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

Osipiuk, J.Tesar, C.Endres, M.Maltseva, N.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 proteaseA, B318Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt)
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9JT
Query on 9JT

Download Ideal Coordinates CCD File 
C [auth A], S [auth B]~{N}-phenyl-2-selanyl-benzamide
C13 H11 N O Se
PVPUYGNPKBMXGO-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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AA [auth B] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , Q [auth B] , 
AA [auth B],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  Q [auth B],  R [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], V [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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D [auth A], T [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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BA [auth B], M [auth A], N [auth A], O [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], U [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth B], P [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.887α = 90
b = 114.887β = 90
c = 252.82γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

View Full Validation Report



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: 2021-03-24
    Type: Initial release