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- PDB-7ve2: Crystal Structure of Lopinavir bound Plasmepsin II (PMII) from Pl... -

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Basic information

Entry
Database: PDB / ID: 7ve2
TitleCrystal Structure of Lopinavir 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-AB1 / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 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 16, 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

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Assembly

Deposited unit
A: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers37,1141
Non-polymers1,8593
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.940, 108.940, 70.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Plasmepsin II


Mass: 37113.926 Da / Num. of mol.: 1
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-AB1 / N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE / ABT-378 / LOPINAVIR


Mass: 628.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
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: 2.81 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→38.52 Å / Num. obs: 6877 / % possible obs: 99.9 % / Redundancy: 7.54 % / Biso Wilson estimate: 87.22 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.95
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 7.57 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 602 / CC1/2: 0.37 / % possible all: 100

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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: 3.2→38.52 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 83.027 / SU ML: 0.637 / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26617 344 5 %RANDOM
Rwork0.22459 ---
obs0.2268 6531 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.423 Å2
Baniso -1Baniso -2Baniso -3
1-5.26 Å2-0 Å2-0 Å2
2--5.26 Å2-0 Å2
3----10.53 Å2
Refinement stepCycle: 1 / Resolution: 3.2→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 130 0 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132813
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172625
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6413847
X-RAY DIFFRACTIONr_angle_other_deg1.11.5736082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2625328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21724.504131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.90815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.205153
X-RAY DIFFRACTIONr_chiral_restr0.0570.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023096
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02614
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_it1.374.9951315
X-RAY DIFFRACTIONr_mcbond_other1.374.9941314
X-RAY DIFFRACTIONr_mcangle_it2.4237.4881642
X-RAY DIFFRACTIONr_mcangle_other2.4237.4891643
X-RAY DIFFRACTIONr_scbond_it1.5265.7741498
X-RAY DIFFRACTIONr_scbond_other1.5225.7511496
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7248.642206
X-RAY DIFFRACTIONr_long_range_B_refined6.98498.47911258
X-RAY DIFFRACTIONr_long_range_B_other6.98598.49411259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 24 -
Rwork0.368 455 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -32.853 Å / Origin y: -13.005 Å / Origin z: 13.987 Å
111213212223313233
T0.0423 Å2-0.1485 Å2-0.0473 Å2-0.5863 Å20.1322 Å2--1.344 Å2
L4.8121 °23.6665 °20.8592 °2-5.4686 °20.3776 °2--2.9266 °2
S-0.0028 Å °-0.5038 Å °0.5395 Å °-0.1372 Å °-0.0022 Å °1.2695 Å °0.3161 Å °-1.2567 Å °0.005 Å °

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