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Basic information

Entry
Database: PDB / ID: 7uoy
TitleNDM1-inhibitor co-structure
ComponentsMetallo beta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Metallo-beta-lactamase inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal 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
: / Chem-O0F / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 Å
AuthorsScapin, G. / Fischmann, T.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates.
Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / ...Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / Young, K. / Flattery, A. / Garlisi, C. / Zhang, R. / Chu, D. / Sheth, P. / Chu, I. / Wu, J. / Markgraf, C. / Kim, H.Y. / Painter, R. / Mayhood, T.W. / DiNunzio, E. / Wyss, D.F. / Buevich, A.V. / Fischmann, T. / Pasternak, A. / Dong, S. / Hicks, J.D. / Villafania, A. / Liang, L. / Murgolo, N. / Black, T. / Hagmann, W.K. / Tata, J. / Parmee, E.R. / Weber, A.E. / Su, J. / Tang, H.
History
DepositionApr 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,80810
Polymers52,5892
Non-polymers1,2198
Water7,494416
1
A: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9045
Polymers26,2951
Non-polymers6104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9045
Polymers26,2951
Non-polymers6104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.074, 78.543, 128.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / Metallobetalactamase NDM-1 / NDM1 ...Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / Metallobetalactamase NDM-1 / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo beta lactamase 1 / New Delhi metallo-beta-lactamase NDM-1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 26294.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaNDM-1, bla NDM-1, blaNDM1, NDM-1, D647_p47098, DDJ63_29735, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3499901_05193, TR3_031, TR4_031
Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-O0F / (6P)-4-amino-6-(2H-tetrazol-5-yl)benzene-1,3-disulfonamide


Mass: 319.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N7O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium acetate 0.1 M sodium acetate pH 4.6 20.0 w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.468→128.034 Å / Num. all: 63605 / Num. obs: 63605 / % possible obs: 93.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.46 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.06 / Rsym value: 0.048 / Net I/av σ(I): 13 / Net I/σ(I): 20.5 / Num. measured all: 336677
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.47-1.554.10.5451.43240179190.2740.6210.5453.181
1.55-1.644.40.4041.93431277210.1960.460.4044.383.4
1.64-1.754.40.2522.93509379100.1270.2930.2526.490.7
1.75-1.94.50.1564.83608879730.0820.1840.1569.897.6
1.9-2.085.60.098.44192275070.0460.110.0917.599.4
2.08-2.326.60.06212.14498468480.030.0770.06226.299.6
2.32-2.686.60.04715.73986260770.0230.0590.04733.499.8
2.68-3.286.10.03321.13145751910.0170.0430.03343.399.7
3.28-4.646.20.02624.92525040680.0130.0320.02657.299.9
4.64-128.0346.40.02426.11530823910.0120.0310.02460.299.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
BUSTER2.11.2refinement
PDB_EXTRACT3.27data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZR9

3zr9


Resolution: 1.47→21.52 Å / Cor.coef. Fo:Fc: 0.9259 / Cor.coef. Fo:Fc free: 0.8978 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.074
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 3201 5.06 %RANDOM
Rwork0.1692 ---
obs0.1706 63312 93.09 %-
Displacement parametersBiso max: 99.81 Å2 / Biso mean: 17.95 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-6.1729 Å20 Å20 Å2
2--0.517 Å20 Å2
3----6.6898 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: final / Resolution: 1.47→21.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 45 417 3877
Biso mean--20.32 26.83 -
Num. residues----461
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1165SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes543HARMONIC5
X-RAY DIFFRACTIONt_it3579HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion473SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4420SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3579HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4893HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion16.02
LS refinement shellResolution: 1.47→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2479 200 5.06 %
Rwork0.2086 3749 -
all0.2106 3949 -
obs--93.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52-0.16850.01110.65360.17180.4060.01650.03360.0521-0.05-0.01010.0298-0.0435-0.0009-0.00640.0194-0.004-0.0035-0.0366-0.0077-0.055-18.424810.1293-14.6107
20.72990.03610.0320.5607-0.00440.53530.00030.0042-0.07720.02420.0016-0.00260.0652-0.0129-0.00190.0208-0.0002-0.0122-0.029-0.0003-0.0755-31.594616.3309-47.4815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A42 - 270
2X-RAY DIFFRACTION2{ B|* }B40 - 270

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