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- PDB-8ex3: Plasmodium falciparum M1 in complex with inhibitor 9aa -

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Basic information

Entry
Database: PDB / ID: 8ex3
TitlePlasmodium falciparum M1 in complex with inhibitor 9aa
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE inhibitor / Malaria / metalloaminopeptidase / inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / nucleus ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain ...Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Chem-X10 / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCalic, P.P.S. / McGowan, S. / Webb, C.T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1185354 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Structure-based development of potent Plasmodium falciparum M1 and M17 aminopeptidase selective and dual inhibitors via S1'-region optimisation.
Authors: Calic, P.P.S. / Vinh, N.B. / Webb, C.T. / Malcolm, T.R. / Ngo, A. / Lowes, K. / Drinkwater, N. / McGowan, S. / Scammells, P.J.
History
DepositionOct 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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: M1 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,72711
Polymers104,8341
Non-polymers89310
Water21,7621208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.440, 108.950, 118.166
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, 1 molecules A

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 104833.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 1218 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-X10 / N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-N~2~-phenylglycinamide


Mass: 429.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-30% poly(ethylene glycol) (PEG)8000, 0.1 M Tris pH 7.5-8.5, 0.2 M MgCl2, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→46.52 Å / Num. obs: 128781 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 17.94 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 6289 / CC1/2: 0.313

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBG

3ebg


Resolution: 1.6→40.05 Å / SU ML: 0.1888 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.3656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 6342 4.93 %
Rwork0.168 122322 -
obs0.1694 128664 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7269 0 55 1208 8532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00757729
X-RAY DIFFRACTIONf_angle_d0.89610505
X-RAY DIFFRACTIONf_chiral_restr0.05521152
X-RAY DIFFRACTIONf_plane_restr0.00641347
X-RAY DIFFRACTIONf_dihedral_angle_d8.33141060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.30941960.30994027X-RAY DIFFRACTION99.95
1.62-1.640.32862000.29454028X-RAY DIFFRACTION99.93
1.64-1.660.29872110.28234030X-RAY DIFFRACTION99.93
1.66-1.680.31421940.27624085X-RAY DIFFRACTION100
1.68-1.70.29562180.26963966X-RAY DIFFRACTION99.95
1.7-1.720.30592120.26494089X-RAY DIFFRACTION99.95
1.72-1.750.29091960.25984035X-RAY DIFFRACTION100
1.75-1.770.29152140.25164039X-RAY DIFFRACTION99.95
1.77-1.80.29552220.26114016X-RAY DIFFRACTION99.98
1.8-1.830.27462210.24014024X-RAY DIFFRACTION100
1.83-1.860.24181950.2284070X-RAY DIFFRACTION100
1.86-1.90.25991850.21074087X-RAY DIFFRACTION99.98
1.9-1.930.21112120.19854052X-RAY DIFFRACTION100
1.93-1.970.23652360.17944023X-RAY DIFFRACTION100
1.97-2.020.20242010.17524053X-RAY DIFFRACTION100
2.02-2.060.20092270.16874053X-RAY DIFFRACTION100
2.06-2.110.20082010.16714068X-RAY DIFFRACTION100
2.11-2.170.20142110.16384063X-RAY DIFFRACTION100
2.17-2.240.20682020.16164062X-RAY DIFFRACTION99.98
2.24-2.310.17852210.15864060X-RAY DIFFRACTION100
2.31-2.390.20572130.16444048X-RAY DIFFRACTION100
2.39-2.490.19362300.16194084X-RAY DIFFRACTION100
2.49-2.60.19842350.16174085X-RAY DIFFRACTION100
2.6-2.740.2232130.15884081X-RAY DIFFRACTION100
2.74-2.910.18131830.16314130X-RAY DIFFRACTION99.98
2.91-3.130.17972410.14944081X-RAY DIFFRACTION100
3.13-3.450.16671930.14054173X-RAY DIFFRACTION100
3.45-3.940.15032040.1264161X-RAY DIFFRACTION100
3.94-4.970.13362210.11664182X-RAY DIFFRACTION100
4.97-40.050.1512340.14984367X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 17.9360024365 Å / Origin y: 112.924390088 Å / Origin z: 128.65660178 Å
111213212223313233
T0.105075864164 Å2-0.0066117470524 Å20.00718795502713 Å2-0.114681166653 Å20.0104213492768 Å2--0.104345280755 Å2
L0.33386847055 °2-0.110435068718 °20.00936364653021 °2-0.620127581359 °20.117396504027 °2--0.502507687887 °2
S-0.0299563301201 Å °-0.0103358114177 Å °0.032206780888 Å °-0.000184963539207 Å °0.00633699062406 Å °-0.0201037581977 Å °-0.0340392295295 Å °0.00546688560093 Å °0.0237972009966 Å °
Refinement TLS groupSelection details: all

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