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- PDB-8tyf: Plasmodium vivax PMV-WM06 inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 8tyf
TitlePlasmodium vivax PMV-WM06 inhibitor complex
ComponentsPlasmepsin V
KeywordsHYDROLASE/Inhibitor / PlasmepsinIX / PlasmepsinX / inhibitor / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / endoplasmic reticulum membrane / proteolysis
Similarity search - Function
Plasmepsin 5 / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / 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 vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsHodder, A.N. / Scally, S.W. / Czabotar, P.E. / Cowman, A.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Plasmodium vivax PMX-XX inhibitor complex
Authors: Hodder, A.N. / Cowman, A.F. / Scally, S.W.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmepsin V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6555
Polymers52,6831
Non-polymers9724
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.720, 81.850, 192.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Plasmepsin V / PvPMV / Plasmepsin 5


Mass: 52682.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PMV, PVX_116695 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A5K302, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: 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.: 2 / 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
#3: Chemical ChemComp-T0F / (2E,4aR,7aS)-6-[(3M)-3-(2-chlorophenyl)pyridin-2-yl]-7a-(2,5-difluorophenyl)-2-imino-3-methyloctahydro-4H-pyrrolo[3,4-d]pyrimidin-4-one


Mass: 467.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20ClF2N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.88 / Details: 20% PEG 3350 0.2M Na2HPO4/KH2PO4

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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: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.59→48.77 Å / Num. obs: 15265 / % possible obs: 99.6 % / Redundancy: 8 % / Biso Wilson estimate: 55.52 Å2 / Rrim(I) all: 0.139 / Net I/σ(I): 12.17
Reflection shellResolution: 2.59→2.687 Å / Mean I/σ(I) obs: 1.54 / Num. unique obs: 1462 / CC1/2: 0.707 / Rpim(I) all: 0.4222 / % possible all: 97.99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→48.77 Å / SU ML: 0.4479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 764 5.01 %
Rwork0.1841 14487 -
obs0.1869 15251 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.79 Å2
Refinement stepCycle: LAST / Resolution: 2.59→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 65 36 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243382
X-RAY DIFFRACTIONf_angle_d0.54794568
X-RAY DIFFRACTIONf_chiral_restr0.043486
X-RAY DIFFRACTIONf_plane_restr0.0028605
X-RAY DIFFRACTIONf_dihedral_angle_d13.60251274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.790.39861490.30962814X-RAY DIFFRACTION98.67
2.8-3.080.28491500.22762851X-RAY DIFFRACTION99.57
3.08-3.520.24491510.19942877X-RAY DIFFRACTION99.77
3.52-4.440.19861540.15352911X-RAY DIFFRACTION99.84
4.44-48.770.2311600.16763034X-RAY DIFFRACTION99.87
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)
13.499616031060.5715419263952.054630924492.10632384315-0.0542997145364.32980578487-0.157071036486-0.3156240742980.06799967498340.1882985200850.101697127212-0.234045913701-0.3279892008430.2454112125390.09454692779170.415411185897-0.0292987408487-0.01988011415840.453140440722-0.04458008139460.33948143694766.4227.97779.794
24.58478148095-0.2796291636361.886146609422.052187160260.3446399516155.624659436110.0793120891023-0.243007379686-0.1229869698380.0159299760805-0.016534496495-0.06302631704610.2565664990030.0828103489-0.06505735887310.451159034833-0.0526142895144-0.05046674953260.4311328416090.03394899344590.33776628004764.78821.42481.896
32.9273937703-0.837338878871-0.8752956382993.445956465421.671840687184.420984627710.101307426494-0.207871758743-0.50318914436-0.00868324590059-0.00582575139250.2528929093610.941190187112-0.576878352474-0.02946055616660.747970239663-0.155959827651-0.1543165627330.4736992121790.0948902770010.49642296312148.9479.36366.022
47.423218458372.366622579931.900019565167.844025718261.0602165956.642484266440.5033533566480.200366835218-0.672479661437-0.244752684977-0.264537063713-0.1265276064560.8546008910270.362051615522-0.2360981736980.810338740086-0.00679423860766-0.1684392007110.6676588521150.06421974659690.39345587235348.1711.82841.781
52.65598402246-0.1687417467020.6803442274021.699659419651.395728645093.721377599530.0416429887683-0.0190943011586-0.0730959039696-0.0869197563999-0.0121401496430.2146478926240.307622079814-0.5602685397170.01892658362050.569942099321-0.123455502552-0.1116638259970.4944047651570.06280525097260.40596562742448.73416.66364.232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:120 )A44 - 120
2X-RAY DIFFRACTION2( CHAIN A AND RESID 121:230 )A121 - 230
3X-RAY DIFFRACTION3( CHAIN A AND RESID 231:335 )A231 - 335
4X-RAY DIFFRACTION4( CHAIN A AND RESID 336:392 )A336 - 392
5X-RAY DIFFRACTION5( CHAIN A AND RESID 393:474 )A393 - 474

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