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- PDB-6tmc: VIM-2_1dh-Triazole inhibitors with promising inhibitor effects ag... -

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Basic information

Entry
Database: PDB / ID: 6tmc
TitleVIM-2_1dh-Triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases
ComponentsBeta-lactamase class B VIM-2
KeywordsANTIBIOTIC / Metallo-beta-lactamase inhibitor / NH-triazole / inhibition properties / crystal structure.
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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
IODIDE ION / Chem-NL5 / HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLeiros, H.-K.S. / Christopeit, T.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273332/2018 Norway
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Structural studies of triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases.
Authors: Muhammad, Z. / Skagseth, S. / Boomgaren, M. / Akhter, S. / Frohlich, C. / Ismael, A. / Christopeit, T. / Bayer, A. / Leiros, H.S.
History
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 10, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9376
Polymers28,3531
Non-polymers5845
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-23 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.805, 63.925, 90.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21A-741-

HOH

31A-757-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Class B carbapenemase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Class B carbapenemase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 28352.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-NL5 / 4-[2-(phenylsulfonyl)ethyl]-5-(propan-2-yloxymethyl)-1~{H}-1,2,3-triazole


Mass: 309.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3O3S / 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: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: HO
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 22-27% PEG 3350 and 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→52.26 Å / Num. obs: 52181 / % possible obs: 98.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.31 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 1.05 / Num. unique obs: 2433

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LSC

5lsc


Resolution: 1.4→52.26 Å / SU ML: 0.1478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.9054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1677 2580 4.94 %
Rwork0.1577 49599 -
obs0.1582 52179 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.87 Å2
Refinement stepCycle: LAST / Resolution: 1.4→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 25 278 2036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211925
X-RAY DIFFRACTIONf_angle_d1.19552652
X-RAY DIFFRACTIONf_chiral_restr0.0784295
X-RAY DIFFRACTIONf_plane_restr0.0063357
X-RAY DIFFRACTIONf_dihedral_angle_d17.5796704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.27461460.28332433X-RAY DIFFRACTION88.05
1.43-1.460.29441500.25572674X-RAY DIFFRACTION98.02
1.46-1.490.23651480.23142705X-RAY DIFFRACTION98.24
1.49-1.520.23181280.21932758X-RAY DIFFRACTION98.46
1.52-1.560.20461440.2022702X-RAY DIFFRACTION97.87
1.56-1.60.24871280.18862734X-RAY DIFFRACTION98.59
1.6-1.650.17751420.16072716X-RAY DIFFRACTION98.31
1.65-1.710.17121610.15712717X-RAY DIFFRACTION98.53
1.71-1.770.16051530.15592766X-RAY DIFFRACTION99.18
1.77-1.840.16241510.13882733X-RAY DIFFRACTION99.14
1.84-1.920.14551240.13732797X-RAY DIFFRACTION99.19
1.92-2.020.14751440.13482742X-RAY DIFFRACTION98.57
2.02-2.150.1572970.13292844X-RAY DIFFRACTION99.59
2.15-2.310.15751520.13892799X-RAY DIFFRACTION99.49
2.31-2.550.15211650.13932792X-RAY DIFFRACTION99.73
2.55-2.920.15491340.15052832X-RAY DIFFRACTION99.03
2.92-3.670.15931470.15382863X-RAY DIFFRACTION100
3.67-52.260.16841660.17042992X-RAY DIFFRACTION99.31

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