8RGJ

Structure of maize adenosine kinase 2 (ADK2) in complex with AMP-PCP

• PDB DOI: https://doi.org/10.2210/pdb8RGJ/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-13 Released: 2025-01-01 
• Deposition Author(s): Morera, S., Kopecny, D., Vigouroux, A.
• Funding Organization(s): Palacky University in Olomouc, Agence Nationale de la Recherche (ANR), Ministry of Education, Youth and Sports of the Czech Republic, Czech Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 
  0.278 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Structure-function study on plant adenosine kinase phosphorylating adenosine and cytokinin ribosides

Kopecny, D.J., Vigouroux, A., Belicek, J., Kopecna, M., Koncitikova, R., Petrik, I., Mik, V., Humplik, J.F., Le Berre, M., Plancqueel, S., Strnad, M., von Schwartzenberg, K., Novak, O., Morera, S., Kopecny, D.

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.

Biological Assembly Evidence: gel filtration, light scattering, SAXS

Macromolecule Content

• Total Structure Weight: 79.42 kDa 
• Atom Count: 5,348 
• Modelled Residue Count: 672 
• Deposited Residue Count: 720 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine kinase	A	360	Zea mays	Mutation(s): 0  Gene Names: ZEAMMB73_Zm00001d017271 EC: 2.7.1.20
UniProt
Find proteins for B4FFH8 (Zea mays) Explore B4FFH8  Go to UniProtKB:  B4FFH8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine kinase	B	360	Zea mays	Mutation(s): 0  Gene Names: ZEAMMB73_Zm00001d017271 EC: 2.7.1.20
UniProt
Find proteins for B4FFH8 (Zea mays) Explore B4FFH8  Go to UniProtKB:  B4FFH8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP (Subject of Investigation/LOI)	C [auth A], F [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.278 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.85	α = 90
b = 135.85	β = 90
c = 78.634	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
autoPROC	data processing
Aimless	data scaling
autoPROC	data processing
BUSTER	refinement
autoPROC	data reduction
FFT	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Morera, S., Kopecny, D., Vigouroux, A.

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Funding Organization	Location	Grant Number
Palacky University in Olomouc	Czech Republic	IGA_PrF_2023_012
Agence Nationale de la Recherche (ANR)	France	ANR-11-IDEX-0003
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.01.01/00/22_008/0004581
Czech Science Foundation	Czech Republic	21-07661S

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release