7M1Y | pdb_00007m1y

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

PDB DOI: https://doi.org/10.2210/pdb7M1Y/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-03-15 Released: 2021-03-24
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Maltseva, N., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.213 (Depositor), 0.217 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (DCC)
R-Value Observed:
0.186 (Depositor)

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.

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.

Macromolecule Content

Total Structure Weight: 74.67 kDa
Atom Count: 5,371
Modeled Residue Count: 626
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease	A, B	318	Severe acute respiratory syndrome coronavirus 2	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9JT (Subject of Investigation/LOI) Query on 9JT Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain C [auth A] MOL2 format, chain S [auth B] MOL2 format, chain C [auth A] mmCIF format, chain S [auth B] mmCIF format, chain C [auth A]	C [auth A], S [auth B]	N-phenyl-2-selanylbenzamide C₁₃ H₁₁ N O Se PVPUYGNPKBMXGO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain L [auth A] SDF format, chain H [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain L [auth A] mmCIF format, chain H [auth A]	AA [auth B] G [auth A] H [auth A] I [auth A] J [auth A] 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		Interactions Focus chain AA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain V [auth B] MOL2 format, chain F [auth A] MOL2 format, chain V [auth B] mmCIF format, chain F [auth A] mmCIF format, chain V [auth B]	F [auth A], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain V [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain D [auth A] MOL2 format, chain T [auth B] MOL2 format, chain D [auth A] mmCIF format, chain T [auth B] mmCIF format, chain D [auth A]	D [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain T [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	BA [auth B], M [auth A], N [auth A], O [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain BA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain U [auth B] MOL2 format, chain E [auth A] MOL2 format, chain U [auth B] mmCIF format, chain E [auth A] mmCIF format, chain U [auth B]	E [auth A], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain U [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain P [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain P [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain P [auth A]	CA [auth B], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain P [auth A] Interactions & Density Focus chain CA [auth B] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.213 (Depositor), 0.217 (DCC)
R-Value Work: 0.184 (Depositor), 0.191 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data:

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.887	α = 90
b = 114.887	β = 90
c = 252.82	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-24

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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 (Full details and data files)

Version 1.0: 2021-03-24
Type: Initial release
Version 1.1: 2023-04-05
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary