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- PDB-6c4g: Plasmepsin V from Plasmodium vivax bound to a transition state mi... -

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Basic information

Entry
Database: PDB / ID: 6c4g
TitlePlasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-601)
ComponentsAspartic protease PM5
KeywordsHYDROLASE / Malaria / protease / inhibitor / plasmepsin
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
WEHI-601 / Chem-EQG / Aspartic protease PM5
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsCzabotar, P.E. / Hodder, A.N. / Nguyen, W. / Sleebs, B.E. / Boddey, J.A. / Cowman, A.F.
Funding support Australia, 6items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1113712 Australia
National Health and Medical Research Council (NHMRC, Australia)121178 Australia
National Health and Medical Research Council (NHMRC, Australia)1117288 Australia
National Health and Medical Research Council (NHMRC, Australia)1092789 Australia
National Health and Medical Research Council (NHMRC, Australia)1079700 Australia
CASS Foundation Science and Medicine GrantSM/15/6430 Australia
CitationJournal: Eur J Med Chem / Year: 2018
Title: Enhanced antimalarial activity of plasmepsin V inhibitors by modification of the P2position of PEXEL peptidomimetics.
Authors: Nguyen, W. / Hodder, A.N. / de Lezongard, R.B. / Czabotar, P.E. / Jarman, K.E. / O'Neill, M.T. / Thompson, J.K. / Jousset Sabroux, H. / Cowman, A.F. / Boddey, J.A. / Sleebs, B.E.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_molecule.asym_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0626
Polymers50,5821
Non-polymers1,4805
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint13 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.541, 91.192, 176.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aspartic protease PM5 / Plasmepsin V


Mass: 50582.363 Da / Num. of mol.: 1 / Fragment: UNP residues 35-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PRR9

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 30 molecules

#4: Chemical ChemComp-EQG / benzyl [(6S,7S,10S,13S,18Z)-18-amino-10-cyclohexyl-6-hydroxy-18-imino-7-(2-methylpropyl)-4,9,12-trioxo-1-phenyl-16-oxa-3,8,11,17-tetraazaoctadecan-13-yl]carbamate


Type: Peptide-like / Mass: 709.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H55N7O7 / Feature type: SUBJECT OF INVESTIGATION / References: WEHI-601
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 25% w/v PEG3350, 0.1 M Bis-Tris chloride, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.39→48.996 Å / Num. obs: 19919 / % possible obs: 99.4 % / Redundancy: 13.301 % / Biso Wilson estimate: 49.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.171 / Χ2: 1.15 / Net I/σ(I): 12.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.39-2.5313.411.6561.4430460.5641.72196.5
2.53-2.7113.4461.1072.3130130.7691.151100
2.71-2.9313.0260.73.7428030.8980.729100
2.93-3.213.9660.3817.225790.9710.395100
3.2-3.5813.5410.19313.9723410.9920.201100
3.58-4.1312.7360.11122.7220970.9970.116100
4.13-5.0513.4130.07334.3417870.9980.076100
5.05-7.113.250.08529.3314090.9980.088100
7.1-48.99611.8530.04941.558440.9990.05299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å49 Å
Translation3.2 Å49 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZL4

4zl4


Resolution: 2.39→48.996 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2381 1990 10.01 %
Rwork0.188 --
obs0.1931 19890 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 50.4578 Å2 / Biso min: 29.9 Å2
Refinement stepCycle: final / Resolution: 2.39→48.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 168 27 3379
Biso mean--59.45 44.84 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093371
X-RAY DIFFRACTIONf_angle_d1.0154552
X-RAY DIFFRACTIONf_chiral_restr0.062487
X-RAY DIFFRACTIONf_plane_restr0.005576
X-RAY DIFFRACTIONf_dihedral_angle_d17.0642003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3903-2.45010.34841270.27421131125891
2.4501-2.51640.31051400.254112701410100
2.5164-2.59040.34031420.256312741416100
2.5904-2.6740.35391400.242412641404100
2.674-2.76960.33611420.241512761418100
2.7696-2.88040.27891420.231812781420100
2.8804-3.01150.28031400.222312541394100
3.0115-3.17030.32871410.207912741415100
3.1703-3.36880.25541440.219612871431100
3.3688-3.62890.24171430.184112941437100
3.6289-3.99390.20861440.165412921436100
3.9939-4.57150.19331450.138913121457100
4.5715-5.75820.171450.154813031448100
5.7582-49.00630.22841550.185913911546100

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