5EJH | pdb_00005ejh

Crystal structure of NAD kinase V98S mutant from Listeria monocytogenes

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
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This is version 2.0 of the entry. See complete history. 


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.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD kinase 1272Listeria monocytogenesMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y8D7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP
Download Ideal Coordinates CCD File 
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 = 62.759α = 90
b = 75.88β = 90
c = 118.207γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • 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