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- PDB-5yia: Crystal Structure of KNI-10343 bound Plasmepsin II (PMII) from Pl... -

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Basic information

Entry
Database: PDB / ID: 5yia
TitleCrystal Structure of KNI-10343 bound Plasmepsin II (PMII) from Plasmodium falciparum
ComponentsPlasmepsin II
KeywordsHYDROLASE / Plasmepsin / Plasmepsin II / KNI-10343 / Aspartic Protease / Plasmodium falciparum / Drug Development / inhibitor
Function / homology
Function and homology information


MHC class II antigen presentation / hemoglobin catabolic process / cytostome / plasmepsin II / Neutrophil degranulation / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / 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
Chem-8V9 / PHOSPHATE ION / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRathore, I. / Mishra, V. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology, Government of IndiaRamalingaswami Re-entry Fellowship India
CitationJournal: Febs J. / Year: 2018
Title: Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights.
Authors: Mishra, V. / Rathore, I. / Arekar, A. / Sthanam, L.K. / Xiao, H. / Kiso, Y. / Sen, S. / Patankar, S. / Gustchina, A. / Hidaka, K. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P.
History
DepositionOct 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,5647
Polymers36,8571
Non-polymers1,7076
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-5 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.080, 106.080, 70.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Plasmepsin II


Mass: 36856.641 Da / Num. of mol.: 1 / Fragment: UNP residues 126-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF14_0077, PF3D7_1408000 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q8I6V3, plasmepsin II

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-8V9 / (4R)-3-[(2S,3S)-3-[[(2R)-2-[2-(4-hydroxyphenyl)ethanoylamino]-3-methylsulfanyl-propanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide


Mass: 720.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H44N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate, 1.26 M ammonium sulfate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54182 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 26651 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3596 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.305 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.143 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20706 1333 5 %RANDOM
Rwork0.16789 ---
obs0.16986 25318 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 2→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 102 199 2901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022802
X-RAY DIFFRACTIONr_bond_other_d0.0030.022591
X-RAY DIFFRACTIONr_angle_refined_deg1.64323829
X-RAY DIFFRACTIONr_angle_other_deg0.9936001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8085337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29725.565124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41215441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.121153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
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_it1.4012.8071321
X-RAY DIFFRACTIONr_mcbond_other1.4012.8061320
X-RAY DIFFRACTIONr_mcangle_it2.3554.1991652
X-RAY DIFFRACTIONr_mcangle_other2.3554.21653
X-RAY DIFFRACTIONr_scbond_it1.6283.1221481
X-RAY DIFFRACTIONr_scbond_other1.593.1141477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6464.5872167
X-RAY DIFFRACTIONr_long_range_B_refined6.73424.1443137
X-RAY DIFFRACTIONr_long_range_B_other6.73524.1423137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 97 -
Rwork0.287 1840 -
obs--100 %
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)
12.6975-0.00391.2651.83330.1571.4618-0.003-0.1228-0.22240.1794-0.02290.04980.23140.10950.02590.15650.02160.03790.06980.05170.100522.4193-37.6818-17.6284
21.6457-1.3801-0.78032.61790.90871.61210.06560.1953-0.2396-0.0558-0.08210.31790.0765-0.14590.01650.0714-0.02090.00130.07370.00650.16142.9872-26.3205-26.8794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 182
2X-RAY DIFFRACTION2A183 - 331

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