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- PDB-7uox: NDM1-inhibitor co-structure -

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Basic information

Entry
Database: PDB / ID: 7uox
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


beta-lactamase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Chem-O0L / NDM-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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)53,88314
Polymers52,5892
Non-polymers1,29412
Water12,070670
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A: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9057
Polymers26,2951
Non-polymers6116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9787
Polymers26,2951
Non-polymers6836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.030, 78.810, 134.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 682 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-O0L / (2M)-4'-(hydroxymethyl)-2-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-ol


Mass: 268.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
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: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.99→134.805 Å / Num. all: 217293 / Num. obs: 217293 / % possible obs: 94.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 5.76 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Rsym value: 0.042 / Net I/av σ(I): 7.9 / Net I/σ(I): 23.9 / Num. measured all: 1408957
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
0.99-1.025.30.3222.272521136820.160.3860.3225.281.3
1.02-1.046.50.2572.797253149450.1160.3030.2577.490.7
1.04-1.076.50.1953.695447147440.090.2320.1959.391.7
1.07-1.116.50.1514.794074144220.070.1810.15111.692.4
1.11-1.146.90.1255.797160141450.0570.150.12514.293.1
1.14-1.186.70.1066.791623136910.050.130.1061693.6
1.18-1.236.50.0957.487124133550.0460.1190.09517.294.5
1.23-1.286.70.0868.386479129160.0410.1080.08619.294.9
1.28-1.346.80.0779.285355124910.0370.0980.07721.695.3
1.34-1.46.60.06710.679430119540.0330.0870.0672495.7
1.4-1.486.50.05912.174601114740.0310.0790.05926.796.5
1.48-1.576.70.0513.973090109610.0260.0680.0531.296.7
1.57-1.676.80.04515.170237103610.0240.0640.04534.797.6
1.67-1.816.50.03916.96319196850.0220.0560.03938.997.8
1.81-1.986.20.03617.75555789800.020.050.03642.397.9
1.98-2.216.30.03318.95146381540.0180.0460.03346.898.3
2.21-2.566.60.03219.54803973220.0170.0430.03250.299.1
2.56-3.136.20.0320.23896662450.0160.0410.0351.799.3
3.13-4.435.90.02919.42908548890.0150.0380.0295399.1
4.43-134.8056.30.03216.31826228770.0160.0420.03254.799.7

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Processing

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

3zr9


Resolution: 0.99→14.49 Å / Cor.coef. Fo:Fc: 0.9726 / Cor.coef. Fo:Fc free: 0.9672 / SU R Cruickshank DPI: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.022 / SU Rfree Blow DPI: 0.023 / SU Rfree Cruickshank DPI: 0.021
RfactorNum. reflection% reflectionSelection details
Rfree0.1482 10920 5.03 %RANDOM
Rwork0.1366 ---
obs0.1372 217086 93.89 %-
Displacement parametersBiso max: 142.46 Å2 / Biso mean: 11.84 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.5057 Å20 Å20 Å2
2---0.0682 Å20 Å2
3----0.4375 Å2
Refine analyzeLuzzati coordinate error obs: 0.097 Å
Refinement stepCycle: final / Resolution: 0.99→14.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 57 702 4327
Biso mean--10.52 22.46 -
Num. residues----482
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1288SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes605HARMONIC5
X-RAY DIFFRACTIONt_it3853HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion520SEMIHARMONIC5
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_contact5257SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3853HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5285HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion5.24
X-RAY DIFFRACTIONt_other_torsion14.45
LS refinement shellResolution: 0.99→1.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 707 5.21 %
Rwork0.1572 12854 -
all0.1578 13561 -
obs--93.89 %
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)
10.35690.0462-0.00960.3912-0.10310.2290.0063-0.01520.03310.0272-0.0052-0.0155-0.02820.01-0.0011-0.0053-0.0008-0.0024-0.01370.0009-0.01431.037310.809515.059
20.4819-0.02020.00320.3424-0.02270.2999-0.0013-0.0004-0.05730.00390.0010.01010.0394-0.01850.0003-0.0199-0.0046-0.0062-0.02720.0017-0.0296-9.8751-23.533617.2499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A30 - 270
2X-RAY DIFFRACTION2{ B|* }B30 - 269

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