5SKW

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1272494722

• PDB DOI: https://doi.org/10.2210/pdb5SKW/pdb
• Deposition Group: G_1002230 (changed state) ExploreG_1002230

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-03 Released: 2022-03-16 
• Deposition Author(s): Imprachim, N., Yosaatmadja, Y., von-Delft, F., Bountra, C., Gileadi, O., Newman, J.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.267 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Literature

PanDDA analysis group deposition

Imprachim, N., Yosaatmadja, Y., von-Delft, F., Bountra, C., Gileadi, O., Newman, J.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 60.13 kDa 
• Atom Count: 4,124 
• Modelled Residue Count: 459 
• Deposited Residue Count: 523 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proofreading exoribonuclease nsp14	A [auth D]	523	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.1.13
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
LF6 (Subject of Investigation/LOI)	B [auth D]	{(1R,2R)-2-[(Z)-(3-methyl-1,2,4-thiadiazol-5(2H)-ylidene)amino]cyclopentyl}methanol C9 H15 N3 O S QUKZXHGECCPEIZ-JGVFFNPUSA-N
PO4	C [auth D], D	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	E [auth D], F [auth D], G [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.267 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.912	α = 90
b = 67.484	β = 90
c = 138.446	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Imprachim, N., Yosaatmadja, Y., von-Delft, F., Bountra, C., Gileadi, O., Newman, J.A.

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Funding Organization	Location	Grant Number
Not funded	United Kingdom	None

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection