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- PDB-9qn6: APH(2'')-IVa with a fragment -

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Basic information

Entry
Database: PDB / ID: 9qn6
TitleAPH(2'')-IVa with a fragment
ComponentsAPH(2'')-Id
KeywordsANTIBIOTIC / inhibitor / complex / enzyme
Function / homology: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / nucleotide binding / Protein kinase-like domain superfamily / metal ion binding / : / APH(2'')-Id
Function and homology information
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuichou, J.F. / Gelin, M. / Tomaszczyk, M. / Kowalewski, J. / Lionne, C.
Funding support France, 3items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionMar 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APH(2'')-Id
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5685
Polymers75,1942
Non-polymers3743
Water1,65792
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7452
Polymers37,5971
Non-polymers1481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8233
Polymers37,5971
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.310, 65.390, 77.420
Angle α, β, γ (deg.)90.00, 91.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APH(2'')-Id


Mass: 37596.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Production host: Escherichia coli (E. coli) / References: UniProt: O68183
#2: Chemical ChemComp-A1I7W / 1~{H}-pyrrolo[2,3-b]pyridin-3-ylmethanol


Mass: 148.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG3350, 50-90 mM Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→49.95 Å / Num. obs: 33269 / % possible obs: 94.27 % / Redundancy: 2.9 % / CC1/2: 0.995 / Net I/σ(I): 13.44
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 3373 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.95 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 1495 4.65 %
Rwork0.2235 --
obs0.2262 32171 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 26 92 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085067
X-RAY DIFFRACTIONf_angle_d0.9176827
X-RAY DIFFRACTIONf_dihedral_angle_d5.805666
X-RAY DIFFRACTIONf_chiral_restr0.053716
X-RAY DIFFRACTIONf_plane_restr0.007906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.39411210.29912900X-RAY DIFFRACTION98
2.37-2.460.33791490.26942890X-RAY DIFFRACTION99
2.46-2.560.34541160.27392916X-RAY DIFFRACTION98
2.56-2.670.34871640.2742716X-RAY DIFFRACTION97
2.69-2.810.30851180.26662548X-RAY DIFFRACTION98
2.81-2.990.34611320.25232845X-RAY DIFFRACTION97
2.99-3.220.33511350.25332946X-RAY DIFFRACTION100
3.22-3.550.2892840.22992678X-RAY DIFFRACTION89
3.55-4.060.26891340.22272369X-RAY DIFFRACTION80
4.06-5.110.22411430.17452919X-RAY DIFFRACTION98
5.11-49.950.22911990.18552949X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°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)
12.9949-0.6867-1.22053.00180.96892.0358-0.1398-0.0579-0.04340.57150.11360.08250.19230.03910.04080.33520.006-0.03180.24650.0610.1629-2.162.329247.965
22.8035-2.1453.86641.9135-2.42746.34890.1877-0.098-0.0857-0.32930.1057-0.09710.5268-0.4332-0.29760.5743-0.0086-0.150.39030.00120.4828-5.0198-6.191920.0008
32.33410.04380.70955.06171.30684.5598-0.04120.06040.2069-0.24480.1032-0.4864-0.33130.1702-0.04290.18880.0006-0.03660.23340.01850.25211.02780.169434.5377
48.3223-1.22792.55254.9616-0.85993.4736-1.0695-0.56020.8425-1.1360.42920.6973-0.8823-0.44720.38490.72980.0326-0.20620.3934-0.030.4559-2.51744.892422.037
53.10971.66011.00245.82791.04713.43050.0910.0970.06250.3042-0.1668-0.44710.02650.01080.0910.24990.0294-0.02780.21940.0410.322550.520916.805981.0846
66.05190.43232.60394.5787-0.26022.40590.1122-0.0776-0.55790.1206-0.18-0.64780.20280.1238-0.18190.38480.0492-0.02210.2310.04850.40547.98428.794276.3948
73.87670.37752.14043.29820.04162.8717-0.15820.57620.3475-0.6882-0.07740.2232-0.09040.1280.22060.43070.05810.04570.23840.02550.25135.371218.729962.3036
83.6347-2.3188-3.23481.92532.47833.7345-0.2932-0.2758-0.3590.45740.13870.35330.91290.2790.19420.88420.07290.05950.32750.01210.418327.45364.221785.4128
93.1163-2.4078-1.02063.34293.52497.4270.629-0.64350.24160.7185-0.34210.15210.1926-1.0699-0.20120.7666-0.10020.3290.5496-0.00910.56612.658213.592593.1628
103.7341.5987-1.35584.6778-1.86941.69340.1986-0.42820.21690.3502-0.03180.35980.07740.0659-0.09240.40470.0172-0.05290.2016-0.05650.277827.4449.909372.1215
113.67731.2124-0.33054.3729-1.34132.08820.092-0.03010.3936-0.3890.0440.6139-0.0228-0.0811-0.15640.42450.0443-0.06250.1994-0.05710.266728.300515.870365.8003
121.5833-0.5250.5566.08872.62295.98170.2279-0.03290.40190.92220.23180.7171-0.51770.3119-0.28450.5855-0.05380.19360.2768-0.10340.487921.924619.186285.0808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 256 )
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 297 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 67 )
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 91 )
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 132 )
8X-RAY DIFFRACTION8chain 'B' and (resid 133 through 161 )
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 181 )
10X-RAY DIFFRACTION10chain 'B' and (resid 182 through 206 )
11X-RAY DIFFRACTION11chain 'B' and (resid 207 through 256 )
12X-RAY DIFFRACTION12chain 'B' and (resid 257 through 297 )

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