9F2H

Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole

PDB DOI: https://doi.org/10.2210/pdb9F2H/pdb

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

Deposited: 2024-04-23 Released: 2024-11-13
Deposition Author(s): Marquez-Monino, M.A., Gonzalez, B., Perez-Canadillas, J.M.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.189
R-Value Work: 0.168
R-Value Observed: 0.169

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.

Marquez-Monino, M.A., Santiveri, C.M., de Leon, P., Camero, S., Campos-Olivas, R., Jimenez, M.A., Saiz, M., Gonzalez, B., Perez-Canadillas, J.M.

(2024) Structure

DOI: https://doi.org/10.1016/j.str.2024.10.025

Macromolecule Content

Total Structure Weight: 50.7 kDa
Atom Count: 4,355
Modelled Residue Count: 435
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	111	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
657 (Subject of Investigation/LOI) Query on 657 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	6-(trifluoromethoxy)-1,3-benzothiazol-2-amine C₈ H₅ F₃ N₂ O S FTALBRSUTCGOEG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth D]	F [auth A], G [auth B], I [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.189
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.056	α = 90
b = 43.383	β = 91.44
c = 109.326	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Marquez-Monino, M.A.

Gonzalez, B.

Perez-Canadillas, J.M.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-117400GB-100
Spanish Ministry of Science, Innovation, and Universities	Spain	MCIN/AEI/10.13039/501100011033

Revision History (Full details and data files)

Version 1.0: 2024-11-13
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

9F2H

Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole

The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)