6IH0

Aquifex aeolicus LpxC complex with ACHN-975


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylase279Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: lpxCenvAaq_1772
EC: 3.5.1.108
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5))
Explore O67648 
Go to UniProtKB:  O67648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67648
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A5F
Query on A5F

Download Ideal Coordinates CCD File 
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
Query on A5U

Download Ideal Coordinates CCD File 
D [auth A]methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate
C11 H22 N2 O4
UTWVEOUYCGZORL-SSDOTTSWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.569α = 90
b = 65.569β = 90
c = 131.595γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81761128016
Other governmentChinaCAMS Innovation Fund for Medical Sciences(2016-12M-3-012)
Other governmentChinaCAMS Innovation Fund for Medical Sciences(2016-12M-3-022)
National Natural Science Foundation of ChinaChina81621064

Revision History  (Full details and data files)

  • 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