8QG5 | pdb_00008qg5

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

PDB DOI: https://doi.org/10.2210/pdb8QG5/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 31.78 kDa
Atom Count: 2,166
Modeled Residue Count: 260
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y8D7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UY6 (Subject of Investigation/LOI) Query on UY6 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]	(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-(phenylmethyl)purin-8-yl]prop-2-ynyl-methyl-amino]methyl]oxolane-3,4-diol C₂₆ H₂₇ N₁₁ O₃ ZVDFDXJRBXGTOT-RRQFZRKBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.853	α = 90
b = 76.192	β = 90
c = 118.92	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.