6RGE

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with an inhibitor

Gelin, M.Labesse, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD kinase 1272Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: nadK1lmo0968
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K1Z
Query on K1Z

Download Ideal Coordinates CCD File 
C [auth A][(2~{R},3~{R},4~{R},5~{R})-2-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] dihydrogen phosphate
C23 H27 N10 O11 P
KWDXFYHXTKUVMJ-MKWZPUSRSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.08α = 90
b = 75.22β = 90
c = 118.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references, Refinement description