PDB-9qos: APH(3')-IIb with an inhibitor

ID or keywords:

Entry

Database: PDB / ID: 9qos

Title

APH(3')-IIb with an inhibitor

Components

Aminoglycoside 3'-phosphotransferase

Keywords

ANTIBIOTIC / inhibitor / complex / enzyme

Function / homology

Function and homology information

kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP binding / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

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

Funding support

France, 3items

Organization	Grant number	Country
Agence Nationale de la Recherche (ANR)	ANR-19-AMRB-0001	France
Agence Nationale de la Recherche (ANR)	(ANR-10-INBS-0004	France
Agence Nationale de la Recherche (ANR)	(ANR-10-INBS-0005	France

Citation

Journal: Commun Chem / Year: 2025
Title: Fragment-based drug design of a bacterial kinase inhibitor capable of increasing the antibiotic sensitivity of clinical isolates.
Authors: Kowalewski, J. / Deutscher, R. / Richardoz, M. / Tomaszczyk, M. / Gelin, M. / Labesse, G. / Hausch, F. / Wright, G.D. / Dunyach-Remy, C. / Guichou, J.F. / Lionne, C.

History

Deposition	Mar 26, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9qos.cif.gz	218.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9qos.ent.gz		Display	PDB format
PDBx/mmJSON format	9qos.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qo/9qos ftp://data.pdbj.org/pub/pdb/validation_reports/qo/9qos	HTTPS FTP

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Related structure data

Related structure data	9qmrC 9qn6C 9qnnC 9qnqC 9qnsC 9qnwC 9qnxC 9qnyC 9qodC 9qoeC 9qokC 9qolC 9qomC 9qp9C 9qpbC 9qpdC 9qplC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4)

Deposited unit

A: Aminoglycoside 3'-phosphotransferase

B: Aminoglycoside 3'-phosphotransferase

hetero molecules

64.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aminoglycoside 3'-phosphotransferase

hetero molecules

defined by author
Evidence: gel filtration
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Aminoglycoside 3'-phosphotransferase

hetero molecules

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.503, 109.666, 124.417
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Aminoglycoside 3'-phosphotransferase Mass: 32023.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aph, PA4119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWR2, kanamycin kinase
#2: Chemical	ChemComp-A1I8B / 5-chloranyl-4-(1~{H}-pyrazol-5-yl)-1~{H}-pyrrolo[2,3-b]pyridine Mass: 218.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₇ClN₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG3350, 50-90 mM Ammonium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9897 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9897 Å / Relative weight: 1
Reflection	Resolution: 1.97→35.18 Å / Num. obs: 72605 / % possible obs: 97.36 % / Redundancy: 1.9 % / CC_1/2: 0.993 / Net I/σ(I): 7.39
Reflection shell	Resolution: 1.97→2.04 Å / Num. unique obs: 3960 / CC_1/2: 0.444

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→35.18 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2528	3691	5.08 %
R_work	0.2128	-	-
obs	0.2149	72605	93.06 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.97→35.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3976	0	30	258	4264

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4116
X-RAY DIFFRACTION	f_angle_d	0.963	5595
X-RAY DIFFRACTION	f_dihedral_angle_d	5.273	611
X-RAY DIFFRACTION	f_chiral_restr	0.056	606
X-RAY DIFFRACTION	f_plane_restr	0.012	786

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.97-2	0.3542	147	0.3246	2655	X-RAY DIFFRACTION	94
2-2.02	0.3334	135	0.3182	2744	X-RAY DIFFRACTION	95
2.02-2.05	0.3458	128	0.3136	2658	X-RAY DIFFRACTION	95
2.05-2.08	0.3683	140	0.3047	2781	X-RAY DIFFRACTION	95
2.08-2.12	0.3184	144	0.2927	2642	X-RAY DIFFRACTION	95
2.12-2.15	0.332	148	0.2934	2736	X-RAY DIFFRACTION	95
2.15-2.19	0.3141	153	0.2753	2665	X-RAY DIFFRACTION	95
2.19-2.23	0.3239	151	0.2929	2684	X-RAY DIFFRACTION	94
2.23-2.27	0.4624	150	0.3628	2616	X-RAY DIFFRACTION	92
2.27-2.32	0.3103	124	0.2836	2714	X-RAY DIFFRACTION	94
2.32-2.37	0.2834	156	0.2521	2691	X-RAY DIFFRACTION	94
2.37-2.42	0.2658	121	0.2423	2654	X-RAY DIFFRACTION	94
2.42-2.48	0.2699	158	0.2487	2680	X-RAY DIFFRACTION	94
2.48-2.55	0.2571	109	0.2333	2733	X-RAY DIFFRACTION	94
2.55-2.62	0.2818	138	0.2176	2612	X-RAY DIFFRACTION	93
2.62-2.71	0.2757	153	0.2173	2646	X-RAY DIFFRACTION	93
2.71-2.81	0.2285	149	0.2164	2687	X-RAY DIFFRACTION	94
2.81-2.92	0.2354	150	0.2031	2646	X-RAY DIFFRACTION	93
2.92-3.05	0.2452	148	0.2047	2643	X-RAY DIFFRACTION	93
3.05-3.21	0.2307	142	0.208	2594	X-RAY DIFFRACTION	92
3.21-3.41	0.2376	158	0.1914	2687	X-RAY DIFFRACTION	94
3.41-3.68	0.234	103	0.1688	2661	X-RAY DIFFRACTION	93
3.68-4.04	0.2184	146	0.1624	2644	X-RAY DIFFRACTION	92
4.05-4.63	0.197	142	0.1472	2482	X-RAY DIFFRACTION	88
4.63-5.83	0.2017	159	0.1707	2443	X-RAY DIFFRACTION	87
5.83-10	0.2031	139	0.1641	2516	X-RAY DIFFRACTION	88

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.6176	-1.7992	-0.6767	5.783	1.4769	1.7996	0.2898	0.2615	0.1208	-0.3412	-0.2975	0.4424	-0.097	-0.3889	-0.0069	0.1347	0.0122	-0.0002	0.2972	-0.0156	0.2588	-6.0881	25.735	20.798
2	1.8031	0.691	-0.7481	1.5168	-0.7137	2.3969	0.07	-0.0356	0.0765	-0.0253	-0.0168	0.0318	-0.143	0.075	-0.0463	0.1987	0.036	-0.0143	0.203	-0.0392	0.1878	10.2028	29.2769	14.7833
3	1.2853	0.1167	-0.8374	2.1603	0.5683	3.3362	0.0179	0.0821	0.0243	-0.2542	0.0145	-0.0287	0.0353	-0.0833	-0.0252	0.1895	-0.0087	0.016	0.1789	0.0083	0.1897	16.1439	27.4453	0.2484
4	2.1079	-2.1851	3.6395	5.9123	-2.4305	7.4183	-0.3905	0.2259	0.2543	-0.9168	0.1893	0.1429	-0.8841	0.7297	0.1797	0.569	-0.1944	-0.0106	0.3618	-0.0041	0.3976	26.952	30.0927	40.6208
5	1.2673	0.1808	0.917	2.7006	0.6529	3.8721	0.0414	0.0948	0.0843	0.1498	-0.0573	-0.1729	-0.2184	0.3573	0.1373	0.1953	0.0271	-0.0014	0.2129	-0.0019	0.1986	23.8245	19.0882	34.5096
6	1.1495	0.2377	0.896	4.0105	0.3428	2.6829	0.1102	-0.1609	-0.2157	0.6109	-0.1737	-0.0376	0.1089	0.1239	0.0152	0.1929	0.0323	0.0249	0.2353	0.0118	0.1636	22.4723	3.7506	36.7132
7	3.872	0.0798	-1.2795	3.2089	-0.2618	2.6577	0.0181	0.0246	0.1773	-0.1794	-0.0999	-0.582	0.1435	0.4001	0.0058	0.2871	0.0882	0.0014	0.2366	-0.0017	0.2947	30.863	5.4662	14.7861
8	1.5465	-0.1598	-0.2463	3.6352	-1.2237	2.4384	-0.0131	0.0033	-0.1201	0.0247	-0.0676	-0.2042	0.1323	0.0897	0.0883	0.1793	0.0298	-0.0337	0.1738	-0.0214	0.2235	24.3404	-2.2294	25.0444

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 130 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 131 through 257 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -5 through 9 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 76 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 77 through 118 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 119 through 170 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 171 through 257 )

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