9FWH | pdb_00009fwh

Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019

• PDB DOI: https://doi.org/10.2210/pdb9FWH/pdb

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


• Deposited: 2024-06-30 Released: 2025-07-09 
• Deposition Author(s): Krojer, T., Kozielski, F., Sele, C., Nyblom, M., Fisher, S.Z., Knecht, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.247 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019

Krojer, T., Kozielski, F., Sele, C., Nyblom, M., Fisher, S.Z., Knecht, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.02 kDa 
• Atom Count: 3,326 
• Modeled Residue Count: 416 
• Deposited Residue Count: 421 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	A	131	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine-N7 methyltransferase nsp14	B	290	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1.56 (PDB Primary Data), 3.1.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IGQ (Subject of Investigation/LOI)	E [auth B]	(4R)-4-phenyl-1,2-thiazolidine 1,1-dioxide C9 H11 N O2 S CAGITIWEIXFGFH-VIFPVBQESA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.247 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.038	α = 90
b = 70.679	β = 90
c = 109.382	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
TRUNCATE	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Krojer, T., Kozielski, F., Sele, C., Nyblom, M., Fisher, S.Z., Knecht, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release