8JUX | pdb_00008jux

Crystal structure of SARS-CoV-2 Papain-like protease complexed with noncovalent inhibitor SR-01

PDB DOI: https://doi.org/10.2210/pdb8JUX/pdb

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

Deposited: 2023-06-27 Released: 2024-07-03
Deposition Author(s): Hsieh, Y.-J., Wu, K.-P.
Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.233 (Depositor), 0.219 (DCC)
R-Value Work:
0.217 (Depositor), 0.215 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of SARS-CoV-2 Papain-like protease complexed with noncovalent inhibitor SR-01

Hsieh, Y.-J., Wu, K.-P.

To be published.

Macromolecule Content

Total Structure Weight: 72.57 kDa
Atom Count: 5,068
Modeled Residue Count: 630
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	A, B	317	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: rep, 1a-1b
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V00 (Subject of Investigation/LOI) Query on V00 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	~{N}-[(3-fluorophenyl)methyl]-1-[(1~{R})-1-(3-methoxynaphthalen-1-yl)ethyl]piperidine-4-carboxamide C₂₆ H₂₉ F N₂ O₂ VMBLTEVHYLOHOW-GOSISDBHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.233 (Depositor), 0.219 (DCC)
R-Value Work: 0.217 (Depositor), 0.215 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.83	α = 90
b = 99.83	β = 90
c = 295.872	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2024-07-03
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.