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

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Basic information

Entry
Database: PDB / ID: 9qpd
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 / 1H-PYRROLO[2,3-B]PYRIDINE / 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 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,5085
Polymers75,1942
Non-polymers3143
Water90150
1
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7933
Polymers37,5971
Non-polymers1962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7152
Polymers37,5971
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.107, 64.553, 72.327
Angle α, β, γ (deg.)90.00, 91.00, 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GVH / 1H-PYRROLO[2,3-B]PYRIDINE


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
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: 0.9897 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 2.3→53.84 Å / Num. obs: 54081 / % possible obs: 96.04 % / Redundancy: 1.8 % / CC1/2: 0.962 / Net I/σ(I): 11.13
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 3155 / CC1/2: 0.629

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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→53.84 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 2666 4.93 %
Rwork0.1978 --
obs0.2003 54081 85.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 22 50 4844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094939
X-RAY DIFFRACTIONf_angle_d0.9946686
X-RAY DIFFRACTIONf_dihedral_angle_d6.164643
X-RAY DIFFRACTIONf_chiral_restr0.054717
X-RAY DIFFRACTIONf_plane_restr0.009865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.3481680.32422785X-RAY DIFFRACTION88
2.34-2.390.3081270.29882796X-RAY DIFFRACTION88
2.39-2.440.31251520.28512764X-RAY DIFFRACTION87
2.44-2.490.3331690.28012803X-RAY DIFFRACTION87
2.49-2.550.35281240.29392763X-RAY DIFFRACTION87
2.55-2.610.31281420.28652727X-RAY DIFFRACTION88
2.61-2.680.30261520.27012707X-RAY DIFFRACTION84
2.68-2.760.33881320.27292663X-RAY DIFFRACTION84
2.76-2.850.32121160.2642733X-RAY DIFFRACTION85
2.85-2.950.30461410.24182661X-RAY DIFFRACTION84
2.95-3.070.3513940.25132548X-RAY DIFFRACTION79
3.07-3.210.32141160.24452578X-RAY DIFFRACTION81
3.21-3.380.27761690.22222763X-RAY DIFFRACTION87
3.38-3.590.28221150.18542784X-RAY DIFFRACTION86
3.59-3.870.2471390.18282720X-RAY DIFFRACTION87
3.87-4.250.21011820.17072654X-RAY DIFFRACTION84
4.26-4.870.17151260.13792653X-RAY DIFFRACTION84
4.87-6.130.22451480.16762533X-RAY DIFFRACTION80
6.14-100.17181540.14382780X-RAY DIFFRACTION88
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)
12.11750.3163-1.39192.2817-1.08085.05640.0373-0.06450.29920.07790.14610.4921-0.0418-0.1097-0.17380.2461-0.0065-0.03460.2988-0.02440.5432-10.2451-11.811337.6011
25.65860.06231.2233.4098-1.00023.7964-0.0945-0.61490.79130.4291-0.2055-0.7152-0.07920.47870.30660.54740.0117-0.16270.36840.04670.514817.6891-2.979139.2142
35.34372.235-0.17195.6578-0.04852.64780.10320.0844-0.5712-0.377-0.0569-0.35480.2811-0.0009-0.03630.32450.0447-0.04090.25290.03250.35923.1344-9.832823.8101
43.5932-1.10642.98063.4878-2.1615.04140.2519-0.2115-0.58320.5816-0.1534-0.31951.23280.3417-0.03790.8430.0543-0.0950.45780.05760.676515.9008-14.078536.4973
52.39380.77911.30842.8890.01952.24110.01340.1776-0.0099-1.0081-0.2540.2436-0.2101-0.2230.2460.62130.1423-0.09490.4636-0.0150.324936.7673-26.0149-14.716
60.00590.1259-0.19714.76761.09694.7665-0.02340.56650.6372-1.295-0.20730.0998-0.6993-0.04430.24650.63350.0923-0.01340.41130.08320.456942.6142-17.0996-11.9473
71.33370.1377-0.28483.5087-0.55342.02930.1823-0.02780.03820.2945-0.2331-0.0132-0.1060.05620.02660.2606-0.0509-0.02230.29730.0590.31942.3152-21.95846.7878
84.383-0.8915-0.09824.75280.96795.56650.2116-0.3781-0.15610.5409-0.3471-0.55490.72410.00950.09060.4674-0.1155-0.09210.470.16070.464451.659-25.600412.3444
96.44450.2804-0.09594.06370.2932.6010.22780.0082-0.5320.2196-0.41440.51590.328-0.05770.16030.4284-0.04260.08820.401-0.01360.49632.0233-28.182312.8431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 132 )
2X-RAY DIFFRACTION2chain 'B' and (resid 133 through 181 )
3X-RAY DIFFRACTION3chain 'B' and (resid 182 through 256 )
4X-RAY DIFFRACTION4chain 'B' and (resid 257 through 297 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 91 )
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 225 )
8X-RAY DIFFRACTION8chain 'A' and (resid 226 through 256 )
9X-RAY DIFFRACTION9chain 'A' and (resid 257 through 297 )

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