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- PDB-9de3: Crystal structure of NDM-1 complexed with compound 28 -

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Basic information

Entry
Database: PDB / ID: 9de3
TitleCrystal structure of NDM-1 complexed with compound 28
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / Inhibitor / Beta-lactamase / complex / NDM
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 28, 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: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1384
Polymers24,6031
Non-polymers5353
Water1,06359
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)42.390, 59.702, 41.643
Angle α, β, γ (deg.)90.00, 97.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 24602.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-A1A4C / {[1-(cyclopentylmethyl)-3-methyl-2-oxo-7-(pyrrolidin-1-yl)-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid


Mass: 404.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N2O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Bis Tris pH 7.5, 25% PEG 3350

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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 PILATUS 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: 2.15→50 Å / Num. obs: 11298 / % possible obs: 98 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.52
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2 / Num. unique obs: 561

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→41.99 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.914 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25564 522 4.6 %RANDOM
Rwork0.22 ---
obs0.22181 10764 94.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.159 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å21.43 Å2
2---0.76 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: 1 / Resolution: 2.15→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 30 59 1791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131777
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151614
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.6592427
X-RAY DIFFRACTIONr_angle_other_deg1.1331.583703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8323.01283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.43158
X-RAY DIFFRACTIONr_chiral_restr0.040.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
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_it5.9354.118915
X-RAY DIFFRACTIONr_mcbond_other5.8964.111914
X-RAY DIFFRACTIONr_mcangle_it7.6336.141142
X-RAY DIFFRACTIONr_mcangle_other7.636.151143
X-RAY DIFFRACTIONr_scbond_it6.284.758862
X-RAY DIFFRACTIONr_scbond_other5.734.514831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8526.5741239
X-RAY DIFFRACTIONr_long_range_B_refined12.42151.0731962
X-RAY DIFFRACTIONr_long_range_B_other10.47349.5691881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.168 Å
RfactorNum. reflection% reflection
Rfree0.325 24 -
Rwork0.329 447 -
obs--55.09 %

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