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- PDB-4y6m: Structure of plasmepsin II from Plasmodium falciparum complexed w... -

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Basic information

Entry
Database: PDB / ID: 4y6m
TitleStructure of plasmepsin II from Plasmodium falciparum complexed with inhibitor PG418
ComponentsPlasmepsin-2
KeywordsHYDROLASE / plasmepsin II Hydroxyethylamine-basd Inhibitor
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-48Q / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsRecacha, R. / Akopjana, I. / Tars, K. / Jaudzems, K.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structures of plasmepsin II from Plasmodium falciparum in complex with two hydroxyethylamine-based inhibitors.
Authors: Recacha, R. / Leitans, J. / Akopjana, I. / Aprupe, L. / Trapencieris, P. / Jaudzems, K. / Jirgensons, A. / Tars, K.
#1: Journal: ACS Med Chem Lett / Year: 2014
Title: Plasmepsin inhibitory activity and structure-guided optimization of a potent hydroxyethylamine-based antimalarial hit.
Authors: Jaudzems, K. / Tars, K. / Maurops, G. / Ivdra, N. / Otikovs, M. / Leitans, J. / Kanepe-Lapsa, I. / Domraceva, I. / Mutule, I. / Trapencieris, P. / Blackman, M.J. / Jirgensons, A.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,33612
Polymers110,8613
Non-polymers2,4759
Water6,900383
1
A: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7794
Polymers36,9541
Non-polymers8253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-2 kcal/mol
Surface area14550 Å2
2
B: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7794
Polymers36,9541
Non-polymers8253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-3 kcal/mol
Surface area14130 Å2
3
C: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7794
Polymers36,9541
Non-polymers8253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-3 kcal/mol
Surface area14870 Å2
Unit cell
Length a, b, c (Å)81.220, 104.600, 111.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA1 - 3291 - 329
2chain BBB2 - 3292 - 329
3chain CCC1 - 3291 - 329

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Components

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


Mass: 36953.734 Da / Num. of mol.: 3 / Fragment: UNP residues 125-453
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-48Q / ~{N}1-[(~{Z},3~{R})-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-but-1-en-2-yl]-5-piperidin-1-yl-~{N}3,~{N}3-dipropyl-benzene-1,3-dicarboxamide


Mass: 640.855 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H52N4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.6 / Details: 0.1 M Sodium citrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.27→77.218 Å / Num. all: 45010 / Num. obs: 45010 / % possible obs: 100 % / Redundancy: 7.1 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.16 / Rsym value: 0.148 / Net I/av σ(I): 4.929 / Net I/σ(I): 11.6 / Num. measured all: 320286
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.27-2.396.10.711.13914664700.310.712.699.9
2.39-2.537.30.5651.34452861360.2240.5653.6100
2.53-2.717.40.4241.84270757910.1670.4244.9100
2.71-2.927.40.292.63965153730.1140.296.9100
2.92-3.27.40.1953.93680149850.0770.1959.9100
3.2-3.587.40.1136.73336745350.0440.11315.4100
3.58-4.147.30.0710.62942340090.0280.0722100
4.14-5.067.30.05312.62501234350.0210.05328.7100
5.06-7.167.10.0768.31920826890.030.07624.7100
7.16-81.226.60.0320.11044315870.0120.0329.1100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJU

2bju


Resolution: 2.27→64.152 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 2286 5.09 %
Rwork0.1716 42647 -
obs0.1741 44933 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.02 Å2 / Biso mean: 31.681 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 2.27→64.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7815 0 177 383 8375
Biso mean--51.16 32.54 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098321
X-RAY DIFFRACTIONf_angle_d1.23611331
X-RAY DIFFRACTIONf_chiral_restr0.0541251
X-RAY DIFFRACTIONf_plane_restr0.0061450
X-RAY DIFFRACTIONf_dihedral_angle_d13.2073012
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4515X-RAY DIFFRACTION7.979TORSIONAL
12B4515X-RAY DIFFRACTION7.979TORSIONAL
13C4515X-RAY DIFFRACTION7.979TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.265-2.31430.3041480.259226142762
2.3143-2.36810.28241520.244725972749
2.3681-2.42730.27891590.223926172776
2.4273-2.4930.26731300.214826482778
2.493-2.56630.26241380.212726392777
2.5663-2.64920.27271260.21226432769
2.6492-2.74390.27551480.199626252773
2.7439-2.85370.23241480.187926432791
2.8537-2.98360.22151380.183126572795
2.9836-3.14090.20521340.168426692803
3.1409-3.33770.21991370.162126662803
3.3377-3.59530.18291190.151626982817
3.5953-3.95710.17911350.140826812816
3.9571-4.52960.18571820.135626572839
4.5296-5.70630.1851310.133327432874
5.7063-64.17720.21341610.168828503011
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)
12.84020.6771.09631.1406-0.15512.6983-0.006-0.1550.08950.0133-0.0540.05660.0712-0.31670.03560.10180.0280.04490.1466-0.00370.111327.7164-23.0258-48.218
20.82070.7258-1.02730.7659-0.7853.06040.0205-0.13750.0460.1073-0.0431-0.07880.15590.29520.03190.15310.0202-0.01350.1711-0.01760.189540.9839-27.967-27.6821
38.1523-1.1736-2.11.35-1.98064.7871-0.13960.5601-0.5402-0.14730.36540.50430.009-0.7317-0.06040.24450.05280.02360.28330.01610.217726.3169-1.4136-9.0684
42.42230.6494-1.22112.16680.2332.35890.02190.0054-0.097-0.1083-0.0532-0.1587-0.05590.18270.01560.15430.004-0.00940.08810.01990.109237.5763-0.8688-5.0593
51.21640.5021-0.11821.78261.04051.33220.0524-0.0505-0.08640.1577-0.11160.10030.1541-0.10830.05460.1916-0.0045-0.00050.16230.01740.110518.4696-15.8294.548
61.9572-0.8885-0.89822.62520.88262.37520.28310.04540.636-0.0926-0.0514-0.3097-0.44080.0053-0.16020.2986-0.00070.08920.19810.08740.3364-7.1959-12.8718-21.7353
72.8885-0.48060.15660.62910.06451.36960.08470.1641-0.1183-0.0138-0.0122-0.035-0.038-0.0851-0.06350.2152-0.02740.0430.15650.02970.14533.0787-32.4179-28.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 177 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 329 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 22 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 177 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 178 through 329 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 201 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 202 through 329 )C0

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