9QOW | pdb_00009qow

APH(2'')-IVa with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb9QOW/pdb

Classification: ANTIBIOTIC
Organism(s): Enterococcus casseliflavus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-26 Released: 2025-11-19
Deposition Author(s): Guichou, J.F., Gelin, M., Tomaszczyk, M., Kowalewski, J., Lionne, C.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

APH(2'')-IVa with an inhibitor

Guichou, J.F., Gelin, M., Tomaszczyk, M., Kowalewski, J., Lionne, C.

To be published.

Macromolecule Content

Total Structure Weight: 76.61 kDa
Atom Count: 4,722
Modeled Residue Count: 592
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APH(2'')-Id	A [auth B], B [auth A]	321	Enterococcus casseliflavus	Mutation(s): 0 Gene Names: aph(2'')-Id
UniProt
Find proteins for O68183 (Enterococcus casseliflavus) Explore O68183 Go to UniProtKB: O68183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O68183
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I8X (Subject of Investigation/LOI) Query on A1I8X Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain E [auth B] MOL2 format, chain L [auth A] MOL2 format, chain E [auth B] mmCIF format, chain L [auth A] mmCIF format, chain E [auth B]	E [auth B], L [auth A]	2-[4-(5-chloranyl-1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,2,3-triazol-1-yl]ethanamide C₁₁ H₉ Cl N₆ O DHQUJKOJRVQESG-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain L [auth A] Interactions & Density Focus chain E [auth B] Focus chain L [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B] D [auth B] F [auth B] G [auth B] H [auth B] C [auth B], D [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth A], K [auth A], M [auth A], N [auth A], O [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.767	α = 90
b = 64.388	β = 91.44
c = 74.064	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-19-AMRB-0001
Agence Nationale de la Recherche (ANR)	France	(ANR-10-INBS-0004
Agence Nationale de la Recherche (ANR)	France	(ANR-10-INBS-0005