9QN6 | pdb_00009qn6

APH(2'')-IVa with a fragment

• PDB DOI: https://doi.org/10.2210/pdb9QN6/pdb

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


• Deposited: 2025-03-24 Released: 2025-12-24 
• Deposition Author(s): Guichou, J.F., Gelin, M., Tomaszczyk, M., Kowalewski, J., Lionne, C.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

APH(2'')-Id with a fragment

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.57 kDa 
• Atom Count: 5,040 
• Modeled Residue Count: 594 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APH(2'')-Id	A, B	321	Enterococcus casseliflavus	Mutation(s): 0  Gene Names: aph(2'')-Id
UniProt
Find proteins for O68183 (Enterococcus casseliflavus) Explore O68183  Go to UniProtKB:  O68183

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I7W (Subject of Investigation/LOI)	C [auth A], D [auth B]	1~{H}-pyrrolo[2,3-b]pyridin-3-ylmethanol C8 H8 N2 O VWPSBHFXPGWHDI-UHFFFAOYSA-N
DMS	E [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.31	α = 90
b = 65.39	β = 91.39
c = 77.42	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Guichou, J.F., Gelin, M., Tomaszczyk, M., Kowalewski, J., Lionne, C.

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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

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release