7IMS | pdb_00007ims

Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z165170770 (Nprot-x0540)

• PDB DOI: https://doi.org/10.2210/pdb7IMS/pdb
• Deposition Group: G_1002353 (changed state) | Explore  G_1002353  

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


• Deposited: 2025-08-11 Released: 2026-08-26 
• Deposition Author(s): Aschenbrenner, J.C., Luptak, J., Balcomb, B.H., Marples, P.G., Bellini, D., Yu, C.W., Douangamath, A., Dias, A., Powell, A., Fearon, D., James, L., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.268 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD)

Luptak, J., Aschenbrenner, J.C., Balcomb, B.H., Marples, P.G., Bellini, D., Yu, C.W., Douangamath, A., Dias, A., Powell, A., Fearon, D., James, L., von Delft, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 13.5 kDa 
• Atom Count: 1,079 
• Modeled Residue Count: 116 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	117	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W0Y (Subject of Investigation/LOI)	B [auth A]	N-methyl-4-sulfamoylbenzamide C8 H10 N2 O3 S CTDFBRMMEMHBEO-UHFFFAOYSA-N
PEG (Subject of Investigation/LOI)	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
IPA (Subject of Investigation/LOI)	D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.268 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.301	α = 90
b = 88.301	β = 90
c = 41.078	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2026-08-26 
Deposition Author(s): Aschenbrenner, J.C., Luptak, J., Balcomb, B.H., Marples, P.G., Bellini, D., Yu, C.W., Douangamath, A., Dias, A., Powell, A., Fearon, D., James, L., von Delft, F.

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release