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- PDB-5yie: Crystal Structure of KNI-10742 bound Plasmepsin II (PMII) from Pl... -

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Basic information

Entry
Database: PDB / ID: 5yie
TitleCrystal Structure of KNI-10742 bound Plasmepsin II (PMII) from Plasmodium falciparum
ComponentsPlasmepsin II
KeywordsHYDROLASE / Plasmepsin / Plasmepsin II / KNI-10742 / Aspartic Protease / Plasmodium falciparum / Drug Development / inhibitor
Function / homology
Function and homology information


hemoglobin catabolic process / cytostome / plasmepsin II / MHC class II antigen presentation / vacuolar lumen / food vacuole / Neutrophil degranulation / 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-8VF / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMishra, V. / Rathore, I. / 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 4, 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

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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)38,7405
Polymers36,7701
Non-polymers1,9714
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-0 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.600, 106.600, 72.200
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: 36769.562 Da / Num. of mol.: 1 / Fragment: UNP residues 127-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF14_0077, PF3D7_1408000 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q8I6V3, plasmepsin II
#2: 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
#3: Chemical ChemComp-8VF / (4R)-3-[(2S,3S)-3-[2-[4-[2-azanylethyl(ethyl)amino]-2,6-dimethyl-phenoxy]ethanoylamino]-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: 717.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H51N5O6S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate

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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: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 23705 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3089 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 10.825 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1185 5 %RANDOM
Rwork0.17284 ---
obs0.17509 22516 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.757 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.1→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 118 142 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022823
X-RAY DIFFRACTIONr_bond_other_d0.0020.022635
X-RAY DIFFRACTIONr_angle_refined_deg1.752.0123873
X-RAY DIFFRACTIONr_angle_other_deg0.98136103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8065336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50525.68125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22115441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.093153
X-RAY DIFFRACTIONr_chiral_restr0.1010.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02622
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_it1.5123.341323
X-RAY DIFFRACTIONr_mcbond_other1.5133.3391322
X-RAY DIFFRACTIONr_mcangle_it2.4255.0021657
X-RAY DIFFRACTIONr_mcangle_other2.4245.0041658
X-RAY DIFFRACTIONr_scbond_it2.1213.7941500
X-RAY DIFFRACTIONr_scbond_other2.1213.7981501
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5195.6252214
X-RAY DIFFRACTIONr_long_range_B_refined6.59628.2853077
X-RAY DIFFRACTIONr_long_range_B_other6.57528.0793045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 87 -
Rwork0.294 1654 -
obs--99.89 %
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)
18.37660.61624.05730.346-0.3624.4373-0.1148-0.4877-0.83510.10870.1110.00640.3709-0.02840.00380.77790.220.25680.33640.28250.570117.155-40.313-12.552
23.7356-1.59450.892.1245-0.07642.43010.00790.0728-0.49790.1549-0.09750.10540.6450.27980.08960.29830.08480.03230.05030.05230.206920.526-36.21-21.739
32.6651-1.8643-0.68082.76680.7532.12530.03430.235-0.585-0.007-0.1120.48020.316-0.24060.07760.1295-0.02960.01880.0582-0.00180.25042.414-24.976-24.375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 31
2X-RAY DIFFRACTION2A32 - 211
3X-RAY DIFFRACTION3A212 - 331

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