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- PDB-9r0x: Crystal structure of NDM-1 with thiol compound 14a -

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Basic information

Entry
Database: PDB / ID: 9r0x
TitleCrystal structure of NDM-1 with thiol compound 14a
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL PROTEIN / inhibitor / thiol / antimicrobial resistance / metall-beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / FOURIER SYNTHESIS / Resolution: 1.13 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)PREDACTED Advanced Grant Agreement no. 101021207European Union
CitationJournal: Eur J Med Chem Rep / Year: 2025
Title: Repurposing of compound libraries yields new inhibitors of NDM-1 metallo-beta-lactamase with diverse zinc-binding moieties
Authors: Kavas, V. / Hinchliffe, P. / Zorman, M. / Krajnc, A. / Proj, M. / Golob, M. / Rambaher, M.H. / Spencer, J. / Gobec, S.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,98311
Polymers52,0912
Non-polymers8939
Water10,088560
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)68.280, 73.448, 76.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#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: 26045.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 5 types, 569 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A1JCJ / ~{N}-(3-chlorophenyl)-2-sulfanyl-ethanamide


Mass: 201.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8ClNOS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.85 Å3/Da / Density % sol: 33.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M NH4SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.13→53.114 Å / Num. obs: 118632 / % possible obs: 89.5 % / Redundancy: 13.4 % / Biso Wilson estimate: 10.97 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 18.8
Reflection shellResolution: 1.13→1.2 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5933 / CC1/2: 0.702 / Rpim(I) all: 0.403

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.13→51.06 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.0228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.146 6072 5.12 %
Rwork0.1187 112560 -
obs0.1201 118632 82.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.9 Å2
Refinement stepCycle: LAST / Resolution: 1.13→51.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 39 560 4001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663770
X-RAY DIFFRACTIONf_angle_d1.00115170
X-RAY DIFFRACTIONf_chiral_restr0.0797562
X-RAY DIFFRACTIONf_plane_restr0.0083702
X-RAY DIFFRACTIONf_dihedral_angle_d13.81321324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.2106220.1865447X-RAY DIFFRACTION9.91
1.14-1.160.2747360.2026904X-RAY DIFFRACTION19.76
1.16-1.170.2244590.20991255X-RAY DIFFRACTION27.89
1.17-1.190.1984860.19711613X-RAY DIFFRACTION35.6
1.19-1.20.24981020.18371937X-RAY DIFFRACTION42.65
1.2-1.220.2026980.17382323X-RAY DIFFRACTION51.07
1.22-1.240.23711530.16912850X-RAY DIFFRACTION63
1.24-1.250.23321830.16623777X-RAY DIFFRACTION82.91
1.25-1.270.18592210.1584084X-RAY DIFFRACTION90.86
1.27-1.30.18912110.14344252X-RAY DIFFRACTION93.56
1.3-1.320.16892380.13214323X-RAY DIFFRACTION94.96
1.32-1.340.15712160.12344311X-RAY DIFFRACTION95.31
1.34-1.370.16222090.1174353X-RAY DIFFRACTION95.62
1.37-1.40.16552320.11594353X-RAY DIFFRACTION95.84
1.4-1.430.14082020.11254382X-RAY DIFFRACTION96.02
1.43-1.460.13572220.10924373X-RAY DIFFRACTION96.23
1.46-1.50.1282560.10344366X-RAY DIFFRACTION96.25
1.5-1.540.13422520.10264393X-RAY DIFFRACTION96.73
1.54-1.580.13882560.1044370X-RAY DIFFRACTION97.02
1.58-1.630.13982720.10144413X-RAY DIFFRACTION96.98
1.63-1.690.13182640.09764391X-RAY DIFFRACTION97.45
1.69-1.760.13872710.10394440X-RAY DIFFRACTION97.72
1.76-1.840.13182730.10264436X-RAY DIFFRACTION97.68
1.84-1.930.14422160.10814519X-RAY DIFFRACTION98.03
1.93-2.060.13772160.10664518X-RAY DIFFRACTION98.46
2.06-2.210.13072730.10594525X-RAY DIFFRACTION98.5
2.22-2.440.13752580.10794544X-RAY DIFFRACTION98.85
2.44-2.790.13472840.11724568X-RAY DIFFRACTION99.18
2.79-3.520.13372560.1214657X-RAY DIFFRACTION99.41
3.52-51.060.16122350.13324883X-RAY DIFFRACTION99.77

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