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- PDB-4zl4: Plasmepsin V from Plasmodium vivax bound to a transition state mi... -

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Basic information

Entry
Database: PDB / ID: 4zl4
TitlePlasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-842)
ComponentsAspartic protease PM5
Keywordshydrolase/hydrolase inhibitor / Malaria / Inhibitor / Aspartyl protease / PEXEL / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Plasmepsin 5 / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide / Chem-4PF / Chem-4PK / Aspartic protease PM5
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsCzabotar, P.E. / Hodder, A.N. / Smith, B.J. / Sleebs, B.E. / Gazdic, M. / Boddey, J.A. / Cowman, A.F.
Funding support Australia, United States, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)637406 Australia
National Health and Medical Research Council (NHMRC, Australia)1057960 Australia
National Health and Medical Research Council (NHMRC, Australia)1010326 Australia
Howard Hughes Medical Institute (HHMI)55007645 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural basis for plasmepsin V inhibition that blocks export of malaria proteins to human erythrocytes.
Authors: Hodder, A.N. / Sleebs, B.E. / Czabotar, P.E. / Gazdik, M. / Xu, Y. / O'Neill, M.T. / Lopaticki, S. / Nebl, T. / Triglia, T. / Smith, B.J. / Lowes, K. / Boddey, J.A. / Cowman, A.F.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartic protease PM5
B: Aspartic protease PM5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,74018
Polymers101,1652
Non-polymers2,57616
Water5,116284
1
A: Aspartic protease PM5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7899
Polymers50,5821
Non-polymers1,2068
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aspartic protease PM5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9529
Polymers50,5821
Non-polymers1,3698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.994, 203.089, 82.165
Angle α, β, γ (deg.)90.00, 121.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-508-

4PF

21B-652-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aspartic protease PM5


Mass: 50582.363 Da / Num. of mol.: 2 / Fragment: unp residues 35-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: Modified pTriex2 / Cell line (production host): High Five / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PRR9

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Non-polymers , 5 types, 300 molecules

#2: Chemical ChemComp-4PK / N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 669.811 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H51N7O7
References: N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-4PF / (2R)-1-[(2R)-2-(2-methoxyethoxy)propoxy]propan-2-amine


Mass: 191.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H21NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsauthors have indicated that the sequence is derived from the PlasmoDB website (http://plasmodb. ...authors have indicated that the sequence is derived from the PlasmoDB website (http://plasmodb.org/plasmo/) record for PmV from P. vivax Sal-1.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.16
Details: 0.11 M (NH4)2SO4, 15.5% PEG4000 0.1 M, 5% Jeffamine M-600, Sodium Acetate/ Acetic Acid pH 4.16

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2014
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.37→41.85 Å / Num. obs: 51893 / % possible obs: 99.22 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.96
Reflection shellResolution: 2.37→2.51 Å / Redundancy: 2.11 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.58 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TZS

1tzs


Resolution: 2.37→41.85 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1990 3.84 %Random selection
Rwork0.1794 ---
obs0.1811 51858 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 168 284 6838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096727
X-RAY DIFFRACTIONf_angle_d1.1599044
X-RAY DIFFRACTIONf_dihedral_angle_d14.9722487
X-RAY DIFFRACTIONf_chiral_restr0.048948
X-RAY DIFFRACTIONf_plane_restr0.0061149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3681-2.42730.36661290.25883521X-RAY DIFFRACTION98
2.4273-2.49290.2861470.23473559X-RAY DIFFRACTION100
2.4929-2.56620.27811370.22663587X-RAY DIFFRACTION100
2.5662-2.64910.27221570.21973569X-RAY DIFFRACTION100
2.6491-2.74370.28981390.21623566X-RAY DIFFRACTION99
2.7437-2.85360.26381450.2113597X-RAY DIFFRACTION100
2.8536-2.98340.25931380.19783567X-RAY DIFFRACTION100
2.9834-3.14060.20961430.19053557X-RAY DIFFRACTION100
3.1406-3.33730.20931440.18643582X-RAY DIFFRACTION100
3.3373-3.59490.22051480.17123575X-RAY DIFFRACTION99
3.5949-3.95640.19771390.15993513X-RAY DIFFRACTION98
3.9564-4.52830.17341390.13793546X-RAY DIFFRACTION99
4.5283-5.70290.19541440.14223547X-RAY DIFFRACTION99
5.7029-41.86020.21031410.1813582X-RAY DIFFRACTION98
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)
12.5620.64760.37333.1960.44281.4185-0.02410.1343-0.0774-0.323-0.09230.2694-0.0019-0.08950.0960.22650.02190.00640.1965-0.02450.17710.70686.63233.939
20.2734-0.61340.13235.08111.26291.1922-0.0238-0.14160.04350.738-0.11040.10070.1491-0.06990.12730.2868-0.0257-0.01320.3070.01640.216.445102.1956.358
30.10530.1346-0.08515.586-5.45925.4022-0.2565-0.3217-0.02880.81180.27890.0419-0.736-0.1086-0.02850.490.0427-0.0940.3716-0.0330.260811.804124.44164.004
41.3421-0.06490.04195.74990.71851.093-0.028-0.0518-0.01130.2506-0.0327-0.16460.05350.08470.05470.2113-0.0081-0.04130.25930.02220.158510.189104.72150.721
52.3742-2.6605-0.97165.19330.01342.0132-0.0891-0.1017-0.26140.13750.18850.80640.139-0.3809-0.02760.1616-0.001-0.01240.35660.01430.2338-10.28250.81231.474
64.97340.42782.06124.5824-0.69712.76410.24620.0406-0.1615-0.75680.1730.66090.0946-0.5108-0.33890.32320.027-0.12430.39080.00430.3594-14.82656.09615.818
73.7859-0.5117-0.54443.6172-0.03124.40110.0920.11190.1164-0.7599-0.09150.1116-0.2419-0.1995-0.00990.32980.043-0.06150.25780.00110.2583-7.06361.28913.799
80.9629-0.88580.39463.8747-0.68660.7614-0.0293-0.08810.19610.0487-0.0118-0.57720.03570.00350.03450.1825-0.0131-0.00760.2719-0.03920.27484.86247.24130.437
91.71472.88420.72066.86711.95280.7275-0.092-0.04480.00860.42230.4134-0.78910.22030.4248-0.32650.34830.0142-0.13750.38880.0080.359715.98819.34540.781
101.1366-0.770.2015.4183-0.00011.4775-0.0368-0.23780.05520.31190.0616-0.32030.0931-0.1142-0.03560.1683-0.029-0.06470.30510.01410.25594.12839.07234.724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:225 )A44 - 225
2X-RAY DIFFRACTION2( CHAIN A AND RESID 226:338 )A226 - 338
3X-RAY DIFFRACTION3( CHAIN A AND RESID 339:372 )A339 - 372
4X-RAY DIFFRACTION4( CHAIN A AND RESID 373:465 )A373 - 465
5X-RAY DIFFRACTION5( CHAIN B AND RESID 44:63 )B44 - 63
6X-RAY DIFFRACTION6( CHAIN B AND RESID 64:109 )B64 - 109
7X-RAY DIFFRACTION7( CHAIN B AND RESID 110:170 )B110 - 170
8X-RAY DIFFRACTION8( CHAIN B AND RESID 171:338 )B171 - 338
9X-RAY DIFFRACTION9( CHAIN B AND RESID 339:372 )B339 - 372
10X-RAY DIFFRACTION10( CHAIN B AND RESID 373:465 )B373 - 465

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