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- PDB-9d5r: Crystal structure of KPC-2 complexed with compound 22 -

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Basic information

Entry
Database: PDB / ID: 9d5r
TitleCrystal structure of KPC-2 complexed with compound 22
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: 1.78 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 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 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)31,6937
Polymers30,8071
Non-polymers8876
Water3,243180
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)56.411, 59.778, 78.317
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-470-

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-A1A14 / {[7-bromo-1-(cyclopentylmethyl)-3-methyl-2-oxo-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid


Mass: 414.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21BrNO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
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: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 25968 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.19
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.77 / Num. unique obs: 1284

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→45.82 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.242 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19142 1280 4.9 %RANDOM
Rwork0.15364 ---
obs0.15551 24653 99.82 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.185 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---1.8 Å2
Refinement stepCycle: 1 / Resolution: 1.78→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 51 180 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151995
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.662922
X-RAY DIFFRACTIONr_angle_other_deg1.4961.5784577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50321.538104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41415324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0781516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
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_it2.7322.2791093
X-RAY DIFFRACTIONr_mcbond_other2.7132.2761092
X-RAY DIFFRACTIONr_mcangle_it3.5853.3981368
X-RAY DIFFRACTIONr_mcangle_other3.5853.4011369
X-RAY DIFFRACTIONr_scbond_it4.4042.7051049
X-RAY DIFFRACTIONr_scbond_other4.1562.6721042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7423.8711543
X-RAY DIFFRACTIONr_long_range_B_refined7.15328.7282491
X-RAY DIFFRACTIONr_long_range_B_other7.00728.3622457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.782→1.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 93 -
Rwork0.185 1781 -
obs--98.48 %

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