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- PDB-5yib: Crystal Structure of KNI-10743 bound Plasmepsin II (PMII) from Pl... -

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Basic information

Entry
Database: PDB / ID: 5yib
TitleCrystal Structure of KNI-10743 bound Plasmepsin II (PMII) from Plasmodium falciparum
ComponentsPlasmepsin II
KeywordsHYDROLASE / Plasmepsin / Plasmepsin II / KNI-10743 / 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-8VC / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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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)38,78810
Polymers36,8571
Non-polymers1,9319
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.250, 106.250, 70.850
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, 123 molecules

#2: Chemical ChemComp-8VC / (4R)-3-[(2S,3S)-3-[2-[4-[2-(dimethylamino)ethyl-methyl-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: 731.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H53N5O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
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: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 21566 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.9
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2 / Num. unique obs: 2723 / % 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: 2.15→39 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 9.802 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19644 1078 5 %RANDOM
Rwork0.17809 ---
obs0.17902 20484 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.15→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 121 114 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022817
X-RAY DIFFRACTIONr_bond_other_d0.0060.022627
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.0033840
X-RAY DIFFRACTIONr_angle_other_deg0.93836077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82125.6125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85915441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.711153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02629
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_it1.1592.9221319
X-RAY DIFFRACTIONr_mcbond_other1.1592.9211318
X-RAY DIFFRACTIONr_mcangle_it1.9664.3781649
X-RAY DIFFRACTIONr_mcangle_other1.9654.3791650
X-RAY DIFFRACTIONr_scbond_it1.4813.2861498
X-RAY DIFFRACTIONr_scbond_other1.483.2881499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.464.832188
X-RAY DIFFRACTIONr_long_range_B_refined5.35124.573010
X-RAY DIFFRACTIONr_long_range_B_other5.35124.5823011
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 80 -
Rwork0.301 1519 -
obs--99.88 %
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)
14.4912-3.4456-3.04117.7724.287412.16430.1315-0.7101-0.1160.56120.08740.213-0.3145-0.0832-0.21890.2231-0.02680.08590.22960.04290.162810.9486-39.214-13.4602
22.8217-0.74241.03181.6096-0.14331.5778-0.0159-0.0347-0.20540.1138-0.05010.05740.15360.11710.0660.18490.01390.0350.10050.02720.104320.3843-36.2623-20.6624
31.8864-1.2992-0.69962.78460.90351.50470.06920.1206-0.30240.0265-0.10320.44020.047-0.1530.0340.0879-0.01440.01670.09450.02370.18311.6124-25.1126-23.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 17
2X-RAY DIFFRACTION2A18 - 220
3X-RAY DIFFRACTION3A221 - 331

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