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- PDB-8w10: Plasmodium vivax PMX-MK7602 inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 8w10
TitlePlasmodium vivax PMX-MK7602 inhibitor complex
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
: / Aspartyl protease, putative
Similarity search - Component
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHodder, A.N. / Scally, S.W. / Cowman, A.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Plasmodium vivax PMX-MK7602 inhibitor complex
Authors: Hodder, A.N. / Cowman, A.F. / Scally, S.W.
History
DepositionFeb 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartyl protease, putative
B: Aspartyl protease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,31911
Polymers85,1602
Non-polymers2,1599
Water93752
1
A: Aspartyl protease, putative
B: Aspartyl protease, putative
hetero molecules

A: Aspartyl protease, putative
B: Aspartyl protease, putative
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 175 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)174,63822
Polymers170,3194
Non-polymers4,31818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Buried area3550 Å2
ΔGint-39 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.310, 88.302, 230.675
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 190 through 197 or (resid 198...
d_2ens_1(chain "B" and (resid 190 through 196 or (resid 197...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISALAALAAA190 - 5377 - 354
d_12NAGNAGNAGNAGCC1
d_13GOLGOLGOLGOLAD701
d_14ZRNZRNZRNZRNAE702
d_21HISHISALAALABB190 - 5377 - 354
d_22NAGNAGNAGNAGBH601
d_23GOLGOLGOLGOLBI602
d_24ZRNZRNZRNZRNBJ603

NCS oper: (Code: givenMatrix: (-0.282651868707, -0.875508340846, -0.391909512803), (-0.751558780976, 0.45601035078, -0.47666965366), (0.596043052015, 0.159811467333, -0.786888159178)Vector: 25. ...NCS oper: (Code: given
Matrix: (-0.282651868707, -0.875508340846, -0.391909512803), (-0.751558780976, 0.45601035078, -0.47666965366), (0.596043052015, 0.159811467333, -0.786888159178)
Vector: 25.1212743401, 23.8881021514, 32.4764828804)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aspartyl protease, putative


Mass: 42579.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PVX_088125 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A5KAC3

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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

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Non-polymers , 4 types, 59 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZRN / (2R,3S)-3-[(2S)-2-amino-4,4-diethyl-6-oxo-1,3-diazinan-1-yl]-N-[(1R,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-2-(methoxymethyl)-2-methyl-2,3-dihydro-1-benzofuran-5-carboxamide


Mass: 520.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Ammonium sulfate 0.1M Sodium HEPES pH7.50 2% PEG 400 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: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.95→38.76 Å / Num. obs: 18136 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 52.29 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.102 / Net I/av σ(I): 8 / Net I/σ(I): 8
Reflection shellResolution: 2.95→3.13 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2861 / CC1/2: 0.577 / Rpim(I) all: 0.482

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TBB

7tbb


Resolution: 2.95→38.76 Å / SU ML: 0.468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 909 5.01 %
Rwork0.1922 17221 -
obs0.1951 18130 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.98 Å2
Refinement stepCycle: LAST / Resolution: 2.95→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 145 53 5577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00575662
X-RAY DIFFRACTIONf_angle_d0.73597703
X-RAY DIFFRACTIONf_chiral_restr0.0518855
X-RAY DIFFRACTIONf_plane_restr0.0065992
X-RAY DIFFRACTIONf_dihedral_angle_d18.24382041
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.68054769777 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.130.36771490.27182792X-RAY DIFFRACTION99.97
3.13-3.380.3011520.2382840X-RAY DIFFRACTION100
3.38-3.720.29821480.2082845X-RAY DIFFRACTION99.93
3.72-4.250.21311420.1622854X-RAY DIFFRACTION100
4.25-5.360.22481490.15052894X-RAY DIFFRACTION100
5.36-38.760.21561690.19692996X-RAY DIFFRACTION99.78

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