9GJZ | pdb_00009gjz

Ntaya methyltransferase (MTase) bound to AT-9010 (2'-methyl-2'-fluoro GTP)

• PDB DOI: https://doi.org/10.2210/pdb9GJZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ntaya virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-23 Released: 2025-09-03 
• Deposition Author(s): Boura, E., Krejcova, K.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Ntaya methyltransferase (MTase) bound to AT-9010 (2'-methyl-2'-fluoro GTP)

Boura, E., Krejcova, K.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.08 kDa 
• Atom Count: 2,521 
• Modeled Residue Count: 262 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	268	Ntaya virus	Mutation(s): 0
UniProt
Find proteins for A0A0C4PNS1 (Ntaya virus) Explore A0A0C4PNS1  Go to UniProtKB:  A0A0C4PNS1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AT9 (Subject of Investigation/LOI)	C [auth A]	[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C11 H17 F N5 O13 P3 GFEXCNGIPRYQFE-GITKWUPZSA-N
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.331	α = 90
b = 71.58	β = 92.635
c = 50.328	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Boura, E., Krejcova, K.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	Program EXCELES, Project No. LX22NPO5103

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release