9HHG | pdb_00009hhg

A rare open conformation for Ubl2 domain of papain-like protease of SARS-CoV2

• PDB DOI: https://doi.org/10.2210/pdb9HHG/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-21 Released: 2025-12-03 
• Deposition Author(s): Freiherr von Scholley, G.L., Schaefer, M., Soler Lopez, M., Hillig, R., Mueller-Dieckmann, C., Kandiah, E.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

A rare open conformation for Ubl2 domain of papain-like protease of SARS-CoV2

Freiherr von Scholley, G.L., Schaefer, M., Soler Lopez, M., Hillig, R., Mueller-Dieckmann, C., Kandiah, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.54 kDa 
• Atom Count: 5,667 
• Modeled Residue Count: 632 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	322	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.09	α = 90
b = 106.517	β = 90
c = 72.329	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Freiherr von Scholley, G.L., Schaefer, M., Soler Lopez, M., Hillig, R., Mueller-Dieckmann, C., Kandiah, E.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	847439

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release