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- PDB-6tta: Haddock model of NDM-1/quercetin complex -

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Basic information

Entry
Database: PDB / ID: 6tta
TitleHaddock model of NDM-1/quercetin complex
ComponentsMetallo beta lactamase NDM-1
KeywordsMETAL BINDING PROTEIN / complex / inhibitor / quercetin / New-Delhi Metallo-beta-lactamase-1 / Haddock / antimicrobial resistance
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
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRiviere, G. / Oueslati, S. / Gayral, M. / Crechet, J.B. / Nhiri, N. / Jacquet, E. / Cintrat, J.C. / Giraud, F. / van Heijenoort, C. / Lescop, E. ...Riviere, G. / Oueslati, S. / Gayral, M. / Crechet, J.B. / Nhiri, N. / Jacquet, E. / Cintrat, J.C. / Giraud, F. / van Heijenoort, C. / Lescop, E. / Pethe, S. / Iorga, B.I. / Naas, T. / Guittet, E. / Morellet, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-33 France
CitationJournal: Acs Omega / Year: 2020
Title: NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-beta-Lactamase-1 and on the Binding with Flavonols as Inhibitors.
Authors: Riviere, G. / Oueslati, S. / Gayral, M. / Crechet, J.B. / Nhiri, N. / Jacquet, E. / Cintrat, J.C. / Giraud, F. / van Heijenoort, C. / Lescop, E. / Pethe, S. / Iorga, B.I. / Naas, T. / Guittet, E. / Morellet, N.
History
DepositionDec 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4084
Polymers23,9751
Non-polymers4333
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area670 Å2
ΔGint-59 kcal/mol
Surface area9700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 23974.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, ...Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, p2146_00143, pCRE380_21, PMK1_ndm00067, PMK1_ndm00076, PMK1_ndm00085, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3531848_05178, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic22D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
132isotropic13D HNCO
142isotropic13D HNCA
152isotropic13D HN(CA)CB
162isotropic13D HN(CO)CA
172isotropic13D HN(COCA)CB
182isotropic13D HN(CA)CO

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Sample preparation

DetailsType: solution / Contents: 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O
Details: Approximately 2.7 micro L of DMSO was added by equivalent of flavonol added to the solution of NDM-1. (the concentration final of DMSO-d6 did not exceed 2.6% in the NMR tube)
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 320 uM / Component: NDM-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
HADDOCKBonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 4

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