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- PDB-1xe5: Structure of plasmepsin II in complex of an pepstatin analogue -

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Basic information

Entry
Database: PDB / ID: 1xe5
TitleStructure of plasmepsin II in complex of an pepstatin analogue
ComponentsPlasmepsin 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cytostome / plasmepsin II / acquisition of nutrients from host / 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
bis-trifluoromethyl pepstatin A ester analogue / Chem-5FE / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPrade, L.
CitationJournal: To be published
Title: Structure of plasmepsin II in complex of an pepstatin analogue
Authors: Prade, L.
History
DepositionSep 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmepsin 2
B: Plasmepsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3554
Polymers73,9072
Non-polymers1,4472
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-37 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.650, 141.650, 98.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Plasmepsin 2 / Aspartic hemoglobinase II / PFAPD


Mass: 36953.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P46925, plasmepsin II
#2: Chemical ChemComp-5FE / 5,5,5-TRIFLUORO-3-HYDROXY-4-[2-(5,5,5-TRIFLUORO-3-HYDROXY-4-{3-METHYL-2-[3-METHYL-2-(3-METHYL-BUTYRYLAMINO)-BUTYRYLAMINO]-BUTYRYLAMINO}-PENTANOYLAMINO)-PROPIONYLAMINO]-PENTANOIC ACID METHYL ESTER


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 723.702 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H47F6N5O9 / References: bis-trifluoromethyl pepstatin A ester analogue
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
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: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.39→119.52 Å / Num. all: 45644 / Num. obs: 45644 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.538 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.265 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25837 2211 5.1 %RANDOM
Rwork0.20029 ---
all0.20314 41389 --
obs0.20314 41389 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.438 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 98 232 5544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225448
X-RAY DIFFRACTIONr_bond_other_d0.0020.024774
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9747424
X-RAY DIFFRACTIONr_angle_other_deg0.792311176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015656
X-RAY DIFFRACTIONr_chiral_restr0.0850.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021074
X-RAY DIFFRACTIONr_nbd_refined0.2040.2986
X-RAY DIFFRACTIONr_nbd_other0.2270.25728
X-RAY DIFFRACTIONr_nbtor_other0.0880.23279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.212
X-RAY DIFFRACTIONr_mcbond_it0.6851.53274
X-RAY DIFFRACTIONr_mcangle_it1.31225332
X-RAY DIFFRACTIONr_scbond_it1.45732174
X-RAY DIFFRACTIONr_scangle_it2.5364.52092
LS refinement shellResolution: 2.385→2.469 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.34 152
Rwork0.291 2794

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