8RF7

Crystal structure of maize adenosine kinase 2 (ADK2) apoform

PDB DOI: https://doi.org/10.2210/pdb8RF7/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.262 (Depositor), 0.249 (DCC)
R-Value Work:
0.234 (Depositor), 0.216 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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., Plancqueel, S., Le Berre, M., Strnad, M., von Schwartzenberg, K., Novak, O., Morera, S., Kopecny, D.

To be published.

Macromolecule Content

Total Structure Weight: 78.85 kDa
Atom Count: 5,310
Modelled Residue Count: 667
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine kinase	A, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4FFH8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.262 (Depositor), 0.249 (DCC)
R-Value Work: 0.234 (Depositor), 0.216 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.222	α = 90
b = 136.222	β = 90
c = 78.226	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Morera, S.

Kopecny, D.

Vigouroux, A.

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	21-07661S
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