8XJH | pdb_00008xjh

Crystal structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2) bound to di-CoA

• PDB DOI: https://doi.org/10.2210/pdb8XJH/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-12-21 Released: 2024-12-25 
• Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.226 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2) bound to di-CoA

Arold, S.T., Hameed, U.F.S.

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: 51.32 kDa 
• Atom Count: 3,522 
• Modeled Residue Count: 399 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase 8	A, B	212	Arabidopsis thaliana	Mutation(s): 0  Gene Names: GNAT8 EC: 2.3.1.48
UniProt
Find proteins for Q9ZV06 (Arabidopsis thaliana) Explore Q9ZV06  Go to UniProtKB:  Q9ZV06

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NG (Subject of Investigation/LOI)	D [auth A], E [auth B]	[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate C42 H70 N14 O32 P6 S2 YAISMNQCMHVVLO-BJLFRJKCSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.226 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.45	α = 90
b = 85.55	β = 90
c = 86.17	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Arold, S.T., Hameed, U.F.S.

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	King Abdullah University of Science and Technology

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release