6IH0

Aquifex aeolicus LpxC complex with ACHN-975

• PDB DOI: https://doi.org/10.2210/pdb6IH0/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-09-27 Released: 2019-01-30 
• Deposition Author(s): Li, D.Y., Fan, S., Jin, Y.Y., Zhang, C., Lv, G.X., Wu, G.T., Yang, Z.Y.
• Funding Organization(s): National Natural Science Foundation of China, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

The Complex Structure of Protein AaLpxC from Aquifex aeolicus with ACHN-975 Molecule Suggests an Inhibitory Mechanism at Atomic-Level against Gram-Negative Bacteria

Fan, S., Li, D., Yan, M., Feng, X., Lv, G., Wu, G., Jin, Y., Wang, Y., Yang, Z.

(2021) Molecules 26

• DOI: https://doi.org/10.3390/molecules26051451

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,552 
• Modelled Residue Count: 267 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A	279	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: lpxC, envA, aq_1772 EC: 3.5.1.108
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5)) Explore O67648  Go to UniProtKB:  O67648

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A5F	B [auth A]	N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide C20 H23 N3 O4 GOCUUDXEOKIQRU-IXDOHACOSA-N
A5U	D [auth A]	methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate C11 H22 N2 O4 UTWVEOUYCGZORL-SSDOTTSWSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.569	α = 90
b = 65.569	β = 90
c = 131.595	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Li, D.Y., Fan, S., Jin, Y.Y., Zhang, C., Lv, G.X., Wu, G.T., Yang, Z.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81761128016
Other government	China	CAMS Innovation Fund for Medical Sciences(2016-12M-3-012)
Other government	China	CAMS Innovation Fund for Medical Sciences(2016-12M-3-022)
National Natural Science Foundation of China	China	81621064

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2021-03-24
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description