4LWB

Structure of Bacillus subtilis nitric oxide synthase in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and biological studies on bacterial nitric oxide synthase inhibitors.

Holden, J.K.Li, H.Jing, Q.Kang, S.Richo, J.Silverman, R.B.Poulos, T.L.

(2013) Proc Natl Acad Sci U S A 110: 18127-18131

  • DOI: 10.1073/pnas.1314080110
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors w ...

    Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors with potential antimicrobial properties. These two compounds impede the growth of B. subtilis under oxidative stress, and crystal structures show that each compound exhibits a unique binding mode. Both compounds serve as excellent leads for the future development of antimicrobials against bacterial NOS-containing bacteria.


    Organizational Affiliation

    Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide synthase oxygenaseA363Bacillus subtilis subsp. subtilis str. 168Mutation(s): 3 
Gene Names: BSU07630nosyflM
EC: 1.14.13.165 (PDB Primary Data), 1.14.14.47 (UniProt)
Find proteins for O34453 (Bacillus subtilis (strain 168))
Explore O34453 
Go to UniProtKB:  O34453
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
QJ8
Query on QJ8

Download CCD File 
A
6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine
C19 H27 N5 O2
NUKSCYDKRQJOFO-WMLDXEAASA-N
 Ligand Interaction
H4B
Query on H4B

Download CCD File 
A
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QJ8Kd:  4400   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.27α = 90
b = 95.078β = 90
c = 62.739γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2013-11-06
    Changes: Database references
  • Version 1.3: 2013-11-20
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description