Download MendeleyCrystal 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.
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
- Funding Organization(s): Agence Nationale de la Recherche (ANR)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.28 Å
- R-Value Free: 0.218 (Depositor), 0.215 (DCC)
- R-Value Work: 0.172 (Depositor), 0.171 (DCC)
- R-Value Observed: 0.175 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NAD kinase 1 | 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 AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UXX (Subject of Investigation/LOI) Query on UXX | 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 Query on CIT | B [auth A] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | ||
| GOL Query on 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), 0.215 (DCC)
- R-Value Work: 0.172 (Depositor), 0.171 (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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHENIX | phasing |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-03-19 Deposition Author(s): Gelin, M., Labesse, G., Lionne, C.
| 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
