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- PDB-8tyh: Plasmodium vivax PMX -

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Basic information

Entry
Database: PDB / ID: 8tyh
TitlePlasmodium vivax PMX
ComponentsAspartyl protease, putative
KeywordsHYDROLASE/Inhibitor / PlasmepsinIX / PlasmepsinX / inhibitor / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homology
Function and homology information


protein processing / aspartic-type endopeptidase activity
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
6-tungstotellurate(VI) / Aspartyl protease, putative
Similarity search - Component
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsHodder, A.N. / Scally, S.W. / Cowman, A.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Febs J. / Year: 2025
Title: Structure-activity analysis of imino-pyrimidinone-fused pyrrolidines aids the development of dual plasmepsin V and plasmepsin X inhibitors.
Authors: Hodder, A.N. / Sleebs, B.E. / Adams, G. / Rezazadeh, S. / Ngo, A. / Jarman, K. / Scally, S. / Czabotar, P. / Wang, H. / McCauley, J.A. / Olsen, D.B. / Cowman, A.F.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartyl protease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5174
Polymers59,5901
Non-polymers1,9283
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.299, 136.299, 45.946
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Aspartyl protease, putative


Mass: 59589.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PVX_088125 / Plasmid: pTriex2 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A5KAC3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M SPG 25% (w/v) PEG 1500 30% (v/v) (+/-)-2-Methyl-2,4-pentanediol 1mM TEW

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→44.61 Å / Num. obs: 43343 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 31.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 1.485 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2639 / CC1/2: 0.712 / Rpim(I) all: 0.471 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→42.82 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2509 2187 5.05 %
Rwork0.228 41140 -
obs0.2292 43327 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.03 Å2
Refinement stepCycle: LAST / Resolution: 1.83→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 51 132 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01872772
X-RAY DIFFRACTIONf_angle_d0.86393829
X-RAY DIFFRACTIONf_chiral_restr0.0476404
X-RAY DIFFRACTIONf_plane_restr0.0031475
X-RAY DIFFRACTIONf_dihedral_angle_d9.72121025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.40581420.33782508X-RAY DIFFRACTION100
1.87-1.910.31751410.31122557X-RAY DIFFRACTION100
1.91-1.960.29931350.30052523X-RAY DIFFRACTION100
1.96-2.010.32971210.27262578X-RAY DIFFRACTION100
2.01-2.070.34061420.28492573X-RAY DIFFRACTION99.96
2.07-2.140.3141260.27932536X-RAY DIFFRACTION100
2.14-2.220.27441900.26022525X-RAY DIFFRACTION100
2.22-2.310.30041200.25512561X-RAY DIFFRACTION99.96
2.31-2.410.25531410.26592564X-RAY DIFFRACTION100
2.41-2.540.28241370.25452572X-RAY DIFFRACTION100
2.54-2.70.2721060.27382614X-RAY DIFFRACTION100
2.7-2.90.29411310.24822567X-RAY DIFFRACTION100
2.91-3.20.28841390.25092563X-RAY DIFFRACTION100
3.2-3.660.24221550.21882586X-RAY DIFFRACTION99.96
3.66-4.610.19141170.17482639X-RAY DIFFRACTION100
4.61-42.820.18461440.17682674X-RAY DIFFRACTION99.82
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)
12.16368920442-0.08609377423740.2031320955714.438912306250.2714399240650.9199577937340.02158319533810.1779840344490.251120349835-0.193686805559-0.0595086294763-0.159289502951-0.1484289297470.08280505037070.04648584174650.2277705942660.00961331140158-0.01754657668990.2767670145260.05112690963860.236187761283-43.2412261302-29.5652407291-4.84087220647
21.999909773270.675569270135-0.676926958543.70011721139-2.651944309012.722003897430.02180492939250.09658035000160.208722409716-0.0559297314463-0.050463454857-0.13629523653-0.0777589965999-0.04511523919230.02480541139960.2804681679090.02170543753220.01111311858790.179863626783-0.0356731152830.360667633741-54.5283586978-8.28238618867-8.72007168198
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 198 through 385 )198 - 3851 - 182
22chain 'A' and (resid 386 through 536 )386 - 536183 - 333

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