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- PDB-9dtj: Crystal structure of KPC-2 complexed with compound 13 -

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Basic information

Entry
Database: PDB / ID: 9dtj
TitleCrystal structure of KPC-2 complexed with compound 13
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / Inhibitor / Beta-lactamase / complex / KPC
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsJacobs, L.M.C. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI103158-01A1 United States
CitationJournal: To Be Published
Title: Hit to Lead Optimization of Heteroaryl Phosphonates Reversible, Broad-Spectrum Inhibitors of Serine and Metallo Carbapenemases.
Authors: Jacobs, L.M.C. / Chen, Y. / Renslo, A.
History
DepositionOct 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3394
Polymers30,8071
Non-polymers5323
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 59.591, 77.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 30806.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-A1A3B / {[6-fluoro-1-methyl-2-oxo-7-(pyrrolidin-1-yl)-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid


Mass: 340.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18FN2O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 26106 / % possible obs: 99 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 34.4
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1266

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→47.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.509 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26981 1297 5 %RANDOM
Rwork0.22624 ---
obs0.2284 24774 98.96 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.691 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---2.48 Å20 Å2
3---3.55 Å2
Refinement stepCycle: 1 / Resolution: 1.77→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 33 165 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132170
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152019
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.662967
X-RAY DIFFRACTIONr_angle_other_deg1.2571.5784636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33721.308107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04615333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8421517
X-RAY DIFFRACTIONr_chiral_restr0.0580.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022522
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4152.6261113
X-RAY DIFFRACTIONr_mcbond_other3.3862.621112
X-RAY DIFFRACTIONr_mcangle_it4.2243.9261400
X-RAY DIFFRACTIONr_mcangle_other4.243.9321401
X-RAY DIFFRACTIONr_scbond_it3.4782.9111057
X-RAY DIFFRACTIONr_scbond_other3.3732.8751024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.684.2161517
X-RAY DIFFRACTIONr_long_range_B_refined6.40531.8152557
X-RAY DIFFRACTIONr_long_range_B_other6.42731.7892456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 109 -
Rwork0.339 1753 -
obs--96.83 %

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