5EJH | pdb_00005ejh

Crystal structure of NAD kinase V98S mutant from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb5EJH/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-11-01 Released: 2016-11-09 
• Deposition Author(s): Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NAD kinase 1 from Listeria monocytogenes: V98S mutant

Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.78 kDa 
• Atom Count: 2,322 
• Modeled Residue Count: 259 
• 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	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.759	α = 90
b = 75.88	β = 90
c = 118.207	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2025-06-11
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary