8QGE | pdb_00008qge

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative

• PDB DOI: https://doi.org/10.2210/pdb8QGE/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-05 Released: 2025-03-19 
• Deposition Author(s): Gelin, M., Labesse, G., Lionne, C.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative

Gelin, M., Labesse, G., Clement, D., Pochet, S., Lionne, C., Leseigneur, C., Huteau, V.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 32.04 kDa 
• Atom Count: 2,244 
• Modeled Residue Count: 261 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase 1	A	272	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: nadK1, lmo0968 EC: 2.7.1.23
UniProt
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8D7  Go to UniProtKB:  Q8Y8D7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UXX (Subject of Investigation/LOI)	D [auth A]	1-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-pent-4-ynyl-amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-ethyl-urea C31 H39 N13 O7 SQXVDVDWDUFQHA-OZZDRAHTSA-N
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.015	α = 90
b = 75.29	β = 90
c = 118.042	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Gelin, M., Labesse, G., Lionne, C.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-17-CE18-0011-02

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release