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- PDB-7dia: Falcilysin in complex with mefloquine -

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Basic information

Entry
Database: PDB / ID: 7dia
TitleFalcilysin in complex with mefloquine
ComponentsFalcilysin
KeywordsPROTEIN BINDING/INHIBITOR / PROTEIN BINDING-INHIBITOR COMPLEX
Function / homology
Function and homology information


hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / metalloendopeptidase activity / protein processing / metal ion binding
Similarity search - Function
Peptidase M16C associated / Peptidase M16C associated / PreP C-terminal domain / Peptidase M16C associated / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like
Similarity search - Domain/homology
ACETATE ION / Chem-H8O / Mefloquine / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLin, J.Q. / El Sahili, A. / Lescar, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Chem Biol / Year: 2024
Title: Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development.
Authors: Wirjanata, G. / Lin, J. / Dziekan, J.M. / El Sahili, A. / Chung, Z. / Tjia, S. / Binte Zulkifli, N.E. / Boentoro, J. / Tham, R. / Jia, L.S. / Go, K.D. / Yu, H. / Partridge, A. / Olsen, D. / ...Authors: Wirjanata, G. / Lin, J. / Dziekan, J.M. / El Sahili, A. / Chung, Z. / Tjia, S. / Binte Zulkifli, N.E. / Boentoro, J. / Tham, R. / Jia, L.S. / Go, K.D. / Yu, H. / Partridge, A. / Olsen, D. / Prabhu, N. / Sobota, R.M. / Nordlund, P. / Lescar, J. / Bozdech, Z.
History
DepositionNov 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conn / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn.ambient_temp / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Description: Ligand geometry / Details: To improve the coordination of zinc ion / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Falcilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,37912
Polymers135,0391
Non-polymers1,34011
Water23,6361312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-33 kcal/mol
Surface area43240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.460, 105.740, 126.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Falcilysin


Mass: 135039.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: FLN / Production host: Escherichia coli (E. coli)
References: UniProt: Q76NL8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 7 types, 1323 molecules

#2: Chemical ChemComp-H8O / (S)-[2,8-bis(trifluoromethyl)quinolin-4-yl]-[(2S)-piperidin-2-yl]methanol


Mass: 378.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16F6N2O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-YMZ / Mefloquine


Mass: 378.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16F6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1312 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate trihydrate pH 7.0, 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→48.77 Å / Num. obs: 180861 / % possible obs: 99.96 % / Redundancy: 13.4 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07683 / Rpim(I) all: 0.02176 / Rrim(I) all: 0.07989 / Net I/σ(I): 23.27
Reflection shellResolution: 1.551→1.606 Å / Redundancy: 13 % / Rmerge(I) obs: 1.397 / Num. unique obs: 17886 / CC1/2: 0.706 / CC star: 0.91 / Rpim(I) all: 0.4002 / % possible all: 99.68

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5M

3s5m


Resolution: 1.55→48.77 Å / SU ML: 0.1789 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 20.3313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 9043 5 %
Rwork0.1742 332768 -
obs0.1753 180852 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8826 0 87 1312 10225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00639229
X-RAY DIFFRACTIONf_angle_d0.893212454
X-RAY DIFFRACTIONf_chiral_restr0.05351350
X-RAY DIFFRACTIONf_plane_restr0.0051593
X-RAY DIFFRACTIONf_dihedral_angle_d17.56243498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.32625760.301410958X-RAY DIFFRACTION98.53
1.57-1.590.30175870.278411193X-RAY DIFFRACTION99.97
1.59-1.610.29225860.270411011X-RAY DIFFRACTION99.97
1.61-1.630.28945820.260511098X-RAY DIFFRACTION99.98
1.63-1.650.2785800.252111052X-RAY DIFFRACTION100
1.65-1.670.27275840.247111154X-RAY DIFFRACTION100
1.67-1.690.24645800.237611090X-RAY DIFFRACTION99.99
1.69-1.720.25175820.228611116X-RAY DIFFRACTION99.99
1.72-1.750.25685850.22411051X-RAY DIFFRACTION99.99
1.75-1.780.26775810.229911116X-RAY DIFFRACTION100
1.78-1.810.24575920.215711162X-RAY DIFFRACTION99.99
1.81-1.840.2375820.206511020X-RAY DIFFRACTION99.98
1.84-1.870.22595790.195311129X-RAY DIFFRACTION100
1.87-1.910.20765850.186311096X-RAY DIFFRACTION100
1.91-1.950.22445880.180711074X-RAY DIFFRACTION99.99
1.95-20.21235850.168911059X-RAY DIFFRACTION99.99
2-2.050.20145870.171111122X-RAY DIFFRACTION100
2.05-2.10.18375900.169711171X-RAY DIFFRACTION99.98
2.1-2.170.20635800.167211050X-RAY DIFFRACTION100
2.17-2.240.19335890.166211076X-RAY DIFFRACTION100
2.24-2.320.19035840.165111092X-RAY DIFFRACTION100
2.32-2.410.19095850.166411082X-RAY DIFFRACTION100
2.41-2.520.19375960.167411147X-RAY DIFFRACTION100
2.52-2.650.19255800.167911058X-RAY DIFFRACTION100
2.65-2.820.19715820.160311088X-RAY DIFFRACTION100
2.82-3.040.16765860.162411113X-RAY DIFFRACTION99.99
3.04-3.340.17765760.157611112X-RAY DIFFRACTION99.99
3.34-3.820.16755850.149211088X-RAY DIFFRACTION100
3.82-4.820.17025870.146811093X-RAY DIFFRACTION100
4.82-48.770.1845870.178511097X-RAY DIFFRACTION99.96

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