6IH0 | pdb_00006ih0

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

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), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

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

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67648
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A5F Query on A5F Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
A5U Query on A5U Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate C₁₁ H₂₂ N₂ O₄ UTWVEOUYCGZORL-SSDOTTSWSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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), 0.165 (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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

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 (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