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- PDB-9d8t: Crystal structure of KPC-2 complexed with compound 16 -

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Basic information

Entry
Database: PDB / ID: 9d8t
TitleCrystal structure of KPC-2 complexed with compound 16
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: 1.97 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
DepositionAug 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 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)31,4915
Polymers30,8071
Non-polymers6844
Water2,414134
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)56.351, 59.794, 78.663
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-452-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-A1A20 / {[7-bromo-1-(cyclopentylmethyl)-2-oxo-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid


Mass: 400.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19BrNO4P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
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-BM / Wavelength: 0.97 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Apr 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 18346 / % possible obs: 95.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 28.22
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 12.03 / Num. unique obs: 928

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→41.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.588 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19803 880 4.8 %RANDOM
Rwork0.15538 ---
obs0.15747 17432 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.957 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å2-0 Å2
2---0.49 Å20 Å2
3---2.1 Å2
Refinement stepCycle: 1 / Resolution: 1.97→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 39 134 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152006
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.652934
X-RAY DIFFRACTIONr_angle_other_deg1.4921.5794600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49921.226106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88715326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1141517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
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_it1.7481.7871098
X-RAY DIFFRACTIONr_mcbond_other1.7361.7821097
X-RAY DIFFRACTIONr_mcangle_it2.5622.661376
X-RAY DIFFRACTIONr_mcangle_other2.5652.6661377
X-RAY DIFFRACTIONr_scbond_it2.5782.1221052
X-RAY DIFFRACTIONr_scbond_other2.5142.1031024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8643.0451516
X-RAY DIFFRACTIONr_long_range_B_refined5.28421.8752493
X-RAY DIFFRACTIONr_long_range_B_other5.19121.7892418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 59 -
Rwork0.139 1307 -
obs--97.64 %

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