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- PDB-7ve0: Crystal Structure of Ritonavir bound Plasmepsin II (PMII) from Pl... -

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Basic information

Entry
Database: PDB / ID: 7ve0
TitleCrystal Structure of Ritonavir bound Plasmepsin II (PMII) from Plasmodium falciparum
ComponentsPlasmepsin II
KeywordsHYDROLASE / Inhibitor / Protease / Peptidomimetic / HIV-1 protease inhibitor / peptidase / hemoglobin degrader
Function / homology
Function and homology information


MHC class II antigen presentation / hemoglobin catabolic process / cytostome / plasmepsin II / vacuolar lumen / Neutrophil degranulation / food vacuole / vacuolar membrane / 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. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RITONAVIR / RITONAVIR / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMishra, V. / Rathore, I. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Ramalingaswami Re-entry Fellowship India
Citation
Journal: Curr Res Struct Biol / Year: 2024
Title: Inhibition of Plasmodium falciparum plasmepsins by drugs targeting HIV-1 protease: A way forward for antimalarial drug discovery.
Authors: Mishra, V. / Deshmukh, A. / Rathore, I. / Chakraborty, S. / Patankar, S. / Gustchina, A. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P.
#1: Journal: Biorxiv / Year: 2023
Title: Molecular insights into the inhibition of plasmepsins by HIV-1 protease inhibitors: Implications for antimalarial drug discovery.
Authors: Mishra, V. / Rathore, I. / Bhaumik, P.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Oct 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 II
B: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,01721
Polymers74,2282
Non-polymers10,78919
Water6,575365
1
A: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,20110
Polymers37,1141
Non-polymers5,0879
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-15 kcal/mol
Surface area14830 Å2
MethodPISA
2
B: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,81611
Polymers37,1141
Non-polymers5,70210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-15 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.290, 70.410, 106.670
Angle α, β, γ (deg.)90.00, 133.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Plasmepsin II


Mass: 37113.926 Da / Num. of mol.: 2 / Mutation: H320Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1408000 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3)pLysS / References: UniProt: Q8I6V3, plasmepsin II
#2: Chemical ChemComp-RIT / RITONAVIR / A-84538


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 720.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H48N6O5S2 / Feature type: SUBJECT OF INVESTIGATION / References: RITONAVIR
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5 M sodium formate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→39.89 Å / Num. obs: 61329 / % possible obs: 95.9 % / Redundancy: 2.89 % / Biso Wilson estimate: 41.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.16
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 8741 / CC1/2: 0.65 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIC

5yic


Resolution: 1.9→39.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.327 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26126 3067 5 %RANDOM
Rwork0.22225 ---
obs0.22448 58262 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.907 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å21.21 Å2
2---5.03 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 567 365 6121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136072
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175733
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.6728391
X-RAY DIFFRACTIONr_angle_other_deg1.081.60313342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5025674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68225.175257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62915885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.774156
X-RAY DIFFRACTIONr_chiral_restr0.0450.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4051.6472654
X-RAY DIFFRACTIONr_mcbond_other0.4051.6472653
X-RAY DIFFRACTIONr_mcangle_it0.7222.4683324
X-RAY DIFFRACTIONr_mcangle_other0.7222.4683325
X-RAY DIFFRACTIONr_scbond_it0.5862.4893418
X-RAY DIFFRACTIONr_scbond_other0.5862.493419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9853.7685062
X-RAY DIFFRACTIONr_long_range_B_refined7.67625.7876400
X-RAY DIFFRACTIONr_long_range_B_other7.65925.1446329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 221 -
Rwork0.356 4206 -
obs--95.25 %
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)
18.1036-1.619715.06616.596-5.122730.8103-0.12-0.2285-0.1685-0.05050.13960.1665-0.1689-0.7154-0.01960.1845-0.0379-0.12660.4468-0.09360.175616.661812.91223.1268
21.55-0.9581-0.53911.59180.11052.71550.06050.1297-0.0521-0.542-0.08550.16310.1677-0.1950.02510.44880.0094-0.2110.5138-0.01740.128926.183918.3592-3.8187
30.82-0.3724-0.00061.4977-1.32524.44390.0212-0.09140.07230.08690.06470.1075-0.4656-0.3507-0.08590.18870.0148-0.11720.4373-0.00960.132923.057226.225623.2797
42.9998-0.2761.24661.8646-1.23376.27140.1881-0.1516-0.1784-0.2712-0.06810.17430.3055-0.4346-0.120.16980.0321-0.14460.4047-0.03720.128219.728222.738113.688
57.46250.07010.49315.91090.44193.627-0.0860.6487-0.4945-0.33480.1183-0.80560.23560.4048-0.03230.19010.035-0.02630.4794-0.08770.3273.5671-22.530422.132
63.01420.2661.03482.5889-0.76971.2666-0.17480.52040.0284-0.21540.0676-0.63480.04210.2050.10720.1150.0033-0.07510.5514-0.01890.33852.4341-12.981427.0853
73.92941.39990.29721.677-0.25941.1968-0.17590.47930.4224-0.19010.08140.115-0.06230.04610.09440.15350.0101-0.14080.48440.02420.1678-23.3307-11.034623.4112
86.60691.5221-1.09482.06690.11423.1812-0.12310.5613-0.0687-0.32850.0609-0.27690.1586-0.03070.06210.19760.0154-0.07650.46640.05080.1836-12.2506-11.026321.1088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 17
2X-RAY DIFFRACTION2A18 - 196
3X-RAY DIFFRACTION3A197 - 277
4X-RAY DIFFRACTION4A278 - 331
5X-RAY DIFFRACTION5B4 - 34
6X-RAY DIFFRACTION6B35 - 218
7X-RAY DIFFRACTION7B219 - 277
8X-RAY DIFFRACTION8B278 - 329

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