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- PDB-1w6h: Novel plasmepsin II-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 1w6h
TitleNovel plasmepsin II-inhibitor complex
ComponentsPLASMEPSIN 2
KeywordsHYDROLASE / MALARIA / DRUG / ASPARTIC PROTEASE / PLASMEPSIN / GLYCOPROTEIN
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
Chem-TIT / Plasmepsin II
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLindberg, J. / Johansson, P.-O. / Rosenquist, A. / Kvarnstroem, I. / Vrang, L. / Samuelsson, B. / Unge, T.
CitationJournal: To be Published
Title: Structural Study of a Novel Inhibitor with Bulky P1 Side Chain in Complex with Plasmepsin II -Implications for Drug Design
Authors: Lindberg, J. / Johansson, P.-O. / Rosenquist, A. / Kvarnstroem, I. / Vrang, L. / Samuelsson, B. / Unge, T.
History
DepositionAug 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,6594
Polymers74,2482
Non-polymers1,4112
Water4,143230
1
A: PLASMEPSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8302
Polymers37,1241
Non-polymers7061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PLASMEPSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8302
Polymers37,1241
Non-polymers7061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.210, 77.614, 84.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PLASMEPSIN 2 / ASPARTIC PROTEASE / ASPARTIC HEMOGLOBINASE II / PFAPD


Mass: 37123.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46925, plasmepsin II
#2: Chemical ChemComp-TIT / N-((3S,4S)-5-[(4-BROMOBENZYL)OXY]-3-HYDROXY-4-{[N-(PYRIDIN-2-YLCARBONYL)-L-VALYL]AMINO}PENTANOYL)-L-ALANYL-L-LEUCINAMIDE


Mass: 705.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H45BrN6O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: HYDROLYSIS OF THE BONDS LINKING CERTAIN HYDROPHOBIC RESIDUES IN HEMOGLOBIN OR ...CATALYTIC ACTIVITY: HYDROLYSIS OF THE BONDS LINKING CERTAIN HYDROPHOBIC RESIDUES IN HEMOGLOBIN OR GLOBIN. ALSO CLEAVES SMALL MOLECULES SUBSTRATES SUCH AS ALA-LEU-GLU-ARG-THR-PHE-|-PHE(NO(2))-SER-PHE-PRO-THR.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.81 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.13375
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13375 Å / Relative weight: 1
ReflectionResolution: 2.2→85 Å / Num. obs: 25914 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.07

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→84.51 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.347 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1377 5 %RANDOM
Rwork0.197 ---
obs0.2 25914 99 %-
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: 33.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å2-0.12 Å2
2---2.41 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.24→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 92 230 5470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225446
X-RAY DIFFRACTIONr_bond_other_d0.0020.024808
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9727412
X-RAY DIFFRACTIONr_angle_other_deg1.142311272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1655656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1480.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025992
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021074
X-RAY DIFFRACTIONr_nbd_refined0.2110.21041
X-RAY DIFFRACTIONr_nbd_other0.2410.25670
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.23248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9521.53272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74925330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11832174
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4234.52082
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 98
Rwork0.238 1732

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