8BWU | pdb_00008bwu

Crystal structure of SARS-CoV-2 nsp14 methyltransferase domain in complex with the SS148 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8BWU/pdb

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


• Deposited: 2022-12-07 Released: 2023-10-11 
• Deposition Author(s): Konkolova, E., Klima, M., Boura, E., Jin, J., Kaniskan, H.U., Han, Y., Vedadi, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 
  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Application of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes

Nigam, A., Hurley, M.F.D., Li, F., Konkolova, E., Klima, M., Trylcova, J., Pollice, R., Cinaroglu, S.S., Levin-Konigsberg, R., Handjaya, J., Schapira, M., Chau, I., Perveen, S., Ng, H.L., Kaniskan, H.U., Han, Y., Singh, S., Gorgulla, C., Kundaje, A., Jin, J., Voelz, V.A., Weber, J., Nencka, R., Boura, E., Vedadi, M., Aspuru-Guzik, A.

(2024) Digit Discov 

• DOI: https://doi.org/10.1039/D4DD00006D

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36 kDa 
• Atom Count: 2,195 
• Modeled Residue Count: 261 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor ETV6,Proofreading exoribonuclease nsp14	A	308	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: ETV6, TEL, TEL1, rep, 1a-1b EC: 3.1.13
UniProt & NIH Common Fund Data Resources
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1
Find proteins for P41212 (Homo sapiens) Explore P41212  Go to UniProtKB:  P41212
PHAROS:  P41212 GTEx:  ENSG00000139083
UniProt Groups	P0DTD1P41212

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NR (Subject of Investigation/LOI)	B [auth A]	(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid C16 H20 N6 O5 S XLTWYAYAFLGUEQ-OPYVMVOTSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.309	α = 90
b = 109.309	β = 90
c = 48.651	γ = 120

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: 2023-10-11 
Deposition Author(s): Konkolova, E., Klima, M., Boura, E., Jin, J., Kaniskan, H.U., Han, Y., Vedadi, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Database references
• Version 1.3: 2024-06-26
  Changes: Database references