8A23

Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383

• PDB DOI: https://doi.org/10.2210/pdb8A23/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-02 Released: 2023-06-14 
• Deposition Author(s): Hanigovsky, M., Krafcikova, P., Klima, M., Boura, E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383

Hanigovsky, M., Krafcikova, P., Klima, M., Boura, E.

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: 47.25 kDa 
• Atom Count: 3,102 
• Modelled Residue Count: 401 
• Deposited Residue Count: 422 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase nsp16	A	299	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1.57
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B	123	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KW6 (Subject of Investigation/LOI)	C [auth A]	(2R,3R,4S,5R)-2-[4-azanyl-5-(2-quinolin-3-ylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol C22 H19 N5 O4 ILUKGDRLISPDRN-WGQQHEPDSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.142	α = 90
b = 85.142	β = 90
c = 162.874	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Hanigovsky, M., Krafcikova, P., Klima, M., Boura, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description