RCSB PDB - 8RPA: Crystal structure of Zea mays adenosine kinase 3 (ZmADK3) in complex with AP5A

 8RPA

Crystal structure of Zea mays adenosine kinase 3 (ZmADK3) in complex with AP5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.257 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AP5Click on this verticalbar to view details

This is version 1.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine kinase361Zea maysMutation(s): 0 
Gene Names: 103646212ZEAMMB73_Zm00001d003017
EC: 2.7.1.20
UniProt
Find proteins for A0A1D6E5Z5 (Zea mays)
Explore A0A1D6E5Z5 
Go to UniProtKB:  A0A1D6E5Z5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D6E5Z5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AP5 (Subject of Investigation/LOI)
Query on AP5

Download Ideal Coordinates CCD File 
B [auth A]BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.257 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.049α = 90
b = 117.49β = 90
c = 165.958γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
BUSTERrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AP5Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic21-07661S
Palacky University in OlomoucCzech RepublicIGA_PrF_2023_012
Agence Nationale de la Recherche (ANR)FranceJean d'Alembert fellowship as part of France 2030 program ANR-11-IDEX-0003

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release