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- PDB-8eye: Plasmodium falciparum M1 in complex with inhibitor 9aj -

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Basic information

Entry
Database: PDB / ID: 8eye
TitlePlasmodium falciparum M1 in complex with inhibitor 9aj
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, C-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 / Zincin-like fold / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase ...Peptidase M1, alanyl aminopeptidase, C-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 / Zincin-like fold / 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. / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-X4I / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 26, 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)106,32717
Polymers104,8341
Non-polymers1,49316
Water20,5371140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.838, 109.294, 117.764
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 , 6 types, 1156 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-X4I / N~2~-(3,5-difluorophenyl)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]glycinamide


Mass: 465.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16F5N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1140 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
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: 0.95373 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.83→46.28 Å / Num. obs: 170846 / % possible obs: 99.74 % / Redundancy: 2 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.68
Reflection shellResolution: 1.83→1.896 Å / Num. unique obs: 16784 / CC1/2: 0.872

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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: 1.83→46.28 Å / SU ML: 0.1945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1911 8299 5.06 %
Rwork0.1564 155694 -
obs0.1582 163993 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.59 Å2
Refinement stepCycle: LAST / Resolution: 1.83→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7219 0 90 1140 8449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767581
X-RAY DIFFRACTIONf_angle_d0.934110276
X-RAY DIFFRACTIONf_chiral_restr0.05561127
X-RAY DIFFRACTIONf_plane_restr0.00671313
X-RAY DIFFRACTIONf_dihedral_angle_d6.60331032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.34162490.29315135X-RAY DIFFRACTION97.47
1.85-1.870.28412750.24015192X-RAY DIFFRACTION99.91
1.87-1.90.25892730.22485187X-RAY DIFFRACTION99.82
1.9-1.920.23912560.21415279X-RAY DIFFRACTION99.96
1.92-1.940.25923080.2065155X-RAY DIFFRACTION99.98
1.94-1.970.22452750.19295220X-RAY DIFFRACTION99.89
1.97-20.25062570.19275186X-RAY DIFFRACTION99.94
2-2.030.21032850.18725193X-RAY DIFFRACTION99.84
2.03-2.060.23553070.18185221X-RAY DIFFRACTION99.8
2.06-2.090.19592740.18055157X-RAY DIFFRACTION99.94
2.09-2.130.21953160.17065200X-RAY DIFFRACTION99.91
2.13-2.170.19842830.16695131X-RAY DIFFRACTION99.61
2.17-2.210.23092890.15335192X-RAY DIFFRACTION99.55
2.21-2.260.19052160.15515208X-RAY DIFFRACTION99.54
2.26-2.310.21622900.16015194X-RAY DIFFRACTION99.44
2.31-2.360.1852650.15855233X-RAY DIFFRACTION99.15
2.36-2.420.21782740.15925091X-RAY DIFFRACTION98.95
2.42-2.480.19962660.15395156X-RAY DIFFRACTION99
2.48-2.560.20073050.1535186X-RAY DIFFRACTION99.98
2.56-2.640.17422690.15515220X-RAY DIFFRACTION100
2.64-2.730.21062890.16045200X-RAY DIFFRACTION99.98
2.73-2.840.21212820.16135164X-RAY DIFFRACTION99.93
2.84-2.970.20032710.15115254X-RAY DIFFRACTION100
2.97-3.130.19392740.1515196X-RAY DIFFRACTION100
3.13-3.330.19162700.14775244X-RAY DIFFRACTION100
3.33-3.580.13592410.13545226X-RAY DIFFRACTION100
3.58-3.940.162990.12995178X-RAY DIFFRACTION99.75
3.94-4.510.16352490.12585193X-RAY DIFFRACTION99.54
4.51-5.680.15422780.13285134X-RAY DIFFRACTION98.74
5.68-46.280.16283140.15615169X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 17.6592511656 Å / Origin y: 4.02314485697 Å / Origin z: 10.2376971196 Å
111213212223313233
T0.109702824036 Å2-0.00495573976254 Å20.0115087352299 Å2-0.124549111984 Å20.0125358004196 Å2--0.116564888301 Å2
L0.418581132436 °2-0.208826077021 °20.032348879093 °2-0.949562754156 °20.214591564108 °2--0.825854955705 °2
S-0.0578264329519 Å °-0.0227775865908 Å °0.0382806007064 Å °0.0189960270197 Å °0.022439131091 Å °-0.0224190745825 Å °-0.0589392280816 Å °0.00371494959362 Å °0.0352757582408 Å °
Refinement TLS groupSelection details: all

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