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- PDB-8ez4: Plasmodium falciparum M17 in complex with inhibitor 9aa -

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Basic information

Entry
Database: PDB / ID: 8ez4
TitlePlasmodium falciparum M17 in complex with inhibitor 9aa
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE inhibitor / Malaria / metalloaminopeptidase / inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Macro domain-like
Similarity search - Domain/homology
CARBONATE ION / Chem-X10 / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 31, 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: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)719,395113
Polymers702,93312
Non-polymers16,461101
Water84,6894701
1
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,76557
Polymers351,4676
Non-polymers8,29851
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,63056
Polymers351,4676
Non-polymers8,16350
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.940, 176.600, 230.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 leucyl aminopeptidase


Mass: 58577.777 Da / Num. of mol.: 12
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: Q8IL11, leucyl aminopeptidase

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Non-polymers , 8 types, 4802 molecules

#2: 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.: 12 / Source method: obtained synthetically / Formula: C22H18F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#6: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4701 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.89→48.47 Å / Num. obs: 556049 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.3
Reflection shellResolution: 1.89→1.96 Å / Num. unique obs: 52897 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
PHENIXv1.20.1-4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 1.89→48.47 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 27706 4.99 %
Rwork0.1774 --
obs0.1793 555296 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47432 0 874 4723 53029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00949233
X-RAY DIFFRACTIONf_angle_d1.18366710
X-RAY DIFFRACTIONf_dihedral_angle_d13.5226906
X-RAY DIFFRACTIONf_chiral_restr0.0667613
X-RAY DIFFRACTIONf_plane_restr0.0098442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.35298120.334515012X-RAY DIFFRACTION86
1.92-1.940.34239660.301717526X-RAY DIFFRACTION100
1.94-1.960.31449360.288917558X-RAY DIFFRACTION100
1.96-1.990.30329310.268117523X-RAY DIFFRACTION100
1.99-2.010.29117950.252317701X-RAY DIFFRACTION100
2.01-2.040.28749270.252317608X-RAY DIFFRACTION100
2.04-2.070.2859920.240817474X-RAY DIFFRACTION100
2.07-2.10.27419530.231817605X-RAY DIFFRACTION100
2.1-2.130.27018510.222517617X-RAY DIFFRACTION100
2.13-2.170.26659370.218917541X-RAY DIFFRACTION100
2.17-2.210.24069110.196917661X-RAY DIFFRACTION100
2.21-2.250.25029050.194717589X-RAY DIFFRACTION100
2.25-2.290.22889140.186517667X-RAY DIFFRACTION100
2.29-2.340.23119590.188717540X-RAY DIFFRACTION100
2.34-2.390.23468850.180417685X-RAY DIFFRACTION100
2.39-2.440.2238850.172617607X-RAY DIFFRACTION100
2.44-2.50.21658970.170117657X-RAY DIFFRACTION100
2.5-2.570.21939620.172117642X-RAY DIFFRACTION100
2.57-2.650.22179180.171817647X-RAY DIFFRACTION100
2.65-2.730.22239240.175517707X-RAY DIFFRACTION100
2.73-2.830.22529380.177317616X-RAY DIFFRACTION100
2.83-2.940.221710170.167317671X-RAY DIFFRACTION100
2.94-3.080.20529680.1717628X-RAY DIFFRACTION100
3.08-3.240.22779420.179317685X-RAY DIFFRACTION100
3.24-3.440.19739460.166617755X-RAY DIFFRACTION100
3.44-3.710.18699360.152817798X-RAY DIFFRACTION100
3.71-4.080.1739480.141517808X-RAY DIFFRACTION100
4.08-4.670.15579130.127617904X-RAY DIFFRACTION100
4.67-5.880.17699020.148618025X-RAY DIFFRACTION100
5.88-48.470.19189360.162418133X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 84.7897 Å / Origin y: 32.2444 Å / Origin z: -35.8082 Å
111213212223313233
T0.2047 Å2-0.0088 Å2-0.0025 Å2-0.193 Å2-0.0125 Å2--0.2356 Å2
L0.0198 °2-0.0077 °20.0034 °2-0.0184 °2-0.005 °2--0.0931 °2
S-0.0029 Å °-0.0069 Å °-0.0273 Å °-0.0037 Å °0.0082 Å °0.0208 Å °-0.0016 Å °0.0041 Å °-0.0055 Å °
Refinement TLS groupSelection details: all

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