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- PDB-9hb0: Crystal structure of Plasmodium falciparum Plasmepsin X in comple... -

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Basic information

Entry
Database: PDB / ID: 9hb0
TitleCrystal structure of Plasmodium falciparum Plasmepsin X in complex with the hydroxyethylamine drug 7k.
ComponentsPlasmepsin X
KeywordsHYDROLASE / Aspartyl protease / hydroxyethylamine inhibitor / complex / non-covalent.
Function / homology
Function and homology information


MHC class II antigen presentation / Neutrophil degranulation / entry into host cell by a symbiont-containing vacuole / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / protein autoprocessing / transport vesicle / protein processing / aspartic-type endopeptidase activity / lysosome / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWithers-Martinez, C. / George, R. / Ogrodowicz, R. / Kunzelmann, S. / Purkiss, A. / Kjaer, S. / Walker, P. / Kovada, V. / Jirgensons, A. / Blackman, M.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)CC2129 United Kingdom
Cancer Research UKCC2129 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Structural Plasticity of Plasmodium falciparum Plasmepsin X to Accommodate Binding of Potent Macrocyclic Hydroxyethylamine Inhibitors.
Authors: Withers-Martinez, C. / George, R. / Ogrodowicz, R. / Kunzelmann, S. / Purkiss, A.G. / Kjaer, S. / Walker, P.A. / Kovada, V. / Jirgensons, A. / Blackman, M.J.
History
DepositionNov 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmepsin X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1093
Polymers40,4271
Non-polymers6822
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-11 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.95, 147.95, 147.95
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

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Components

#1: Protein Plasmepsin X / PfPMX / Plasmepsin 10


Mass: 40426.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PMX, PF3D7_0808200
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q8IAS0, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-A1ITU / (4S)-4-[(1R)-2-[2-(3-methoxyphenyl)propan-2-ylamino]-1-oxidanyl-ethyl]-16-propyl-3,16-diazatricyclo[16.3.1.1^{6,10}]tricosa-1(21),6,8,10(23),18(22),19-hexaene-2,17-dione


Mass: 585.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H47N3O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 20% [w/v] PEG 4000, 0.2 M Magnesium sulfate, 10% [w/v] Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→104.62 Å / Num. obs: 59002 / % possible obs: 100 % / Redundancy: 40.4 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.022 / Rrim(I) all: 0.102 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-104.62370.0424470.9990.0090.043
1.7-1.7340.26.87331260.3031.5577.047

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→104.616 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.823 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2265 2835 4.806 %
Rwork0.1952 56157 -
all0.197 --
obs-58992 99.997 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→104.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 48 199 2785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122800
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162491
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.8013828
X-RAY DIFFRACTIONr_angle_other_deg0.8241.7155760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.929.68816
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg6.3651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08410426
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.78610123
X-RAY DIFFRACTIONr_chiral_restr0.1040.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023286
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02650
X-RAY DIFFRACTIONr_nbd_refined0.1870.2448
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.22202
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.2169
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4380.216
X-RAY DIFFRACTIONr_nbd_other0.1490.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0830.214
X-RAY DIFFRACTIONr_mcbond_it3.1522.8271386
X-RAY DIFFRACTIONr_mcbond_other3.152.8271386
X-RAY DIFFRACTIONr_mcangle_it4.3335.061745
X-RAY DIFFRACTIONr_mcangle_other4.3355.0631746
X-RAY DIFFRACTIONr_scbond_it4.1463.1461414
X-RAY DIFFRACTIONr_scbond_other4.1213.1381411
X-RAY DIFFRACTIONr_scangle_it5.8955.6372079
X-RAY DIFFRACTIONr_scangle_other5.8665.6212074
X-RAY DIFFRACTIONr_lrange_it8.2929.0873000
X-RAY DIFFRACTIONr_lrange_other8.25827.7072953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.3272100.36141010.35943110.9140.9041000.359
1.744-1.7920.3322180.32340040.32442220.9250.9331000.314
1.792-1.8440.3342070.28638820.28840890.940.9481000.267
1.844-1.9010.2661830.25738150.25839980.9540.9581000.227
1.901-1.9630.2492220.22936560.2338780.960.9661000.197
1.963-2.0320.2161460.21736070.21737530.9690.971000.185
2.032-2.1090.2591510.21334520.21536030.9590.9711000.182
2.109-2.1950.2111900.19833100.19835000.9720.9761000.17
2.195-2.2920.2131700.19231880.19333580.970.9771000.165
2.292-2.4040.2261600.19330150.19431750.9720.9771000.168
2.404-2.5340.2371330.19129130.19330460.9640.9771000.168
2.534-2.6880.2321250.19527880.19629130.9710.9761000.176
2.688-2.8730.231280.19125570.19326850.9690.9781000.176
2.873-3.1030.2171310.18724290.18825600.9710.9791000.177
3.103-3.3990.1981030.18822120.18823150.9770.981000.187
3.399-3.80.24870.1820370.18221240.9670.9811000.19
3.8-4.3870.155750.16918090.16818840.9850.9831000.191
4.387-5.370.194890.1515030.15215920.980.9871000.182
5.37-7.5850.256540.2212050.22112590.9740.9771000.261
7.585-104.6160.313530.2336740.2387290.9280.96499.72570.309
Refinement TLS params.Method: refined / Origin x: 62.9095 Å / Origin y: 24.0416 Å / Origin z: -20.8567 Å
111213212223313233
T0.0329 Å20.0196 Å2-0.0119 Å2-0.0796 Å20.0015 Å2--0.0213 Å2
L2.5224 °20.1668 °21.0357 °2-1.0967 °20.5496 °2--1.3684 °2
S-0.0173 Å °-0.2871 Å °-0.1103 Å °-0.0964 Å °-0.0238 Å °0.1107 Å °-0.0563 Å °-0.2808 Å °0.0411 Å °
Refinement TLS groupSelection: ALL

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