3E27 | pdb_00003e27

Nicotinic acid mononucleotide (NaMN) adenylyltransferase from Bacillus anthracis: product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.273 (Depositor) 
  • R-Value Work: 
    0.201 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3E27

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD.

Sorci, L.Pan, Y.Eyobo, Y.Rodionova, I.Huang, N.Kurnasov, O.Zhong, S.MacKerell, A.D.Zhang, H.Osterman, A.L.

(2009) Chem Biol 16: 849-861

  • DOI: https://doi.org/10.1016/j.chembiol.2009.07.006
  • Primary Citation Related Structures: 
    3E27, 3HFJ

  • PubMed Abstract: 

    The emergence of multidrug-resistant pathogens necessitates the search for new antibiotics acting on previously unexplored targets. Nicotinate mononucleotide adenylyltransferase of the NadD family, an essential enzyme of NAD biosynthesis in most bacteria, was selected as a target for structure-based inhibitor development. Using iterative in silico and in vitro screens, we identified small molecule compounds that efficiently inhibited target enzymes from Escherichia coli (ecNadD) and Bacillus anthracis (baNadD) but had no effect on functionally equivalent human enzymes. On-target antibacterial activity was demonstrated for some of the selected inhibitors. A 3D structure of baNadD was solved in complex with one of these inhibitors (3_02), providing mechanistic insights and guidelines for further improvement. Most importantly, the results of this study help validate NadD as a target for the development of antibacterial agents with potential broad-spectrum activity.


  • Organizational Affiliation
    • Burnham Institute for Medical Research, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 90.69 kDa 
  • Atom Count: 6,870 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 756 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinate (Nicotinamide) nucleotide adenylyltransferase
A, B, C, D
189Bacillus anthracisMutation(s): 0 
Gene Names: nadDBT9727_4068
EC: 2.7.7.18

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DND

Query on DND



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
NICOTINIC ACID ADENINE DINUCLEOTIDE
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.273 (Depositor) 
  • R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.856α = 90
b = 137.413β = 90
c = 143.972γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-06-11
    Changes: Database references
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description