4NZ9 | pdb_00004nz9

Crystal Structure of FabI from S. aureus in complex with a novel benzimidazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4NZ9/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Staphylococcus aureus subsp. aureus USA300
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-11 Released: 2014-12-31 
• Deposition Author(s): Mehboob, S., Johnson, M.E., Santarsiero, B.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.278 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

To be published

Mehboob, S., Truong, L., Santarsiero, B.D., Johnson, M.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.24 kDa 
• Atom Count: 4,193 
• Modeled Residue Count: 509 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADPH]	A, B	279	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0  Gene Names: fabi, SAUSA300_0912 EC: 1.3.1.39
UniProt
Find proteins for A0A0H2XIJ1 (Staphylococcus aureus (strain USA300)) Explore A0A0H2XIJ1  Go to UniProtKB:  A0A0H2XIJ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
1JT	C [auth A], E [auth B]	1-(4-methoxy-3-methylbenzyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole C20 H22 N2 O BBFOREFQNPCWBB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.278 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.545	α = 90
b = 61.034	β = 90
c = 112.609	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Mehboob, S., Johnson, M.E., Santarsiero, B.D.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description