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- PDB-7di7: Falcilysin in complex with chloroquine -

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Basic information

Entry
Database: PDB / ID: 7di7
TitleFalcilysin in complex with chloroquine
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-CLQ / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 / software / 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_distant_solvent_atoms.auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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_R_work / _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 / _software.classification / _software.name / _software.version / _struct_conn.ptnr2_auth_seq_id / _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)135,5435
Polymers135,0391
Non-polymers5034
Water26,9141494
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 area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.940, 106.610, 127.810
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

#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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CLQ / N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE / CHLOROQUINE


Mass: 319.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26ClN3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1494 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.09 %
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 8.0, 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: 1.82→49.2 Å / Num. obs: 115028 / % possible obs: 99.94 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1393 / Net I/σ(I): 16.88
Reflection shellResolution: 1.821→1.887 Å / Rmerge(I) obs: 1.347 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 11325 / CC1/2: 0.7 / % possible all: 99.61

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Processing

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

3s5m


Resolution: 1.82→49.2 Å / SU ML: 0.2285 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 20.0209
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1984 11045 4.98 %
Rwork0.176 210563 -
obs0.1771 115014 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.82→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8857 0 31 1494 10382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659110
X-RAY DIFFRACTIONf_angle_d0.814512274
X-RAY DIFFRACTIONf_chiral_restr0.05151338
X-RAY DIFFRACTIONf_plane_restr0.00461568
X-RAY DIFFRACTIONf_dihedral_angle_d16.19823458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.38493700.33366931X-RAY DIFFRACTION98.57
1.84-1.860.36173650.29956969X-RAY DIFFRACTION99.99
1.86-1.890.32443660.28277063X-RAY DIFFRACTION99.99
1.89-1.910.33733740.32017081X-RAY DIFFRACTION99.88
1.91-1.940.37813630.30766952X-RAY DIFFRACTION99.88
1.94-1.960.26033700.23787009X-RAY DIFFRACTION100
1.96-1.990.24853700.2177049X-RAY DIFFRACTION99.99
1.99-2.020.22813640.20746983X-RAY DIFFRACTION99.96
2.02-2.050.23193670.19997038X-RAY DIFFRACTION99.97
2.05-2.080.23123690.19667059X-RAY DIFFRACTION99.97
2.09-2.120.2243680.19147029X-RAY DIFFRACTION100
2.12-2.160.21153650.18927005X-RAY DIFFRACTION100
2.16-2.20.22153640.19067038X-RAY DIFFRACTION99.97
2.2-2.250.24053640.20787022X-RAY DIFFRACTION99.76
2.25-2.290.24163690.20646987X-RAY DIFFRACTION99.62
2.29-2.350.20683670.17447038X-RAY DIFFRACTION100
2.35-2.410.18893710.17177038X-RAY DIFFRACTION100
2.41-2.470.20423630.17127014X-RAY DIFFRACTION100
2.47-2.540.20563740.16837021X-RAY DIFFRACTION99.99
2.54-2.630.20363680.16696953X-RAY DIFFRACTION100
2.63-2.720.2043690.16577061X-RAY DIFFRACTION100
2.72-2.830.21673690.16986997X-RAY DIFFRACTION100
2.83-2.960.19113720.1687075X-RAY DIFFRACTION100
2.96-3.110.193710.1647009X-RAY DIFFRACTION100
3.11-3.310.16563690.15577026X-RAY DIFFRACTION100
3.31-3.560.17433660.14927019X-RAY DIFFRACTION99.99
3.57-3.920.15273720.1437040X-RAY DIFFRACTION99.96
3.92-4.490.13033680.1337019X-RAY DIFFRACTION100
4.49-5.660.17293640.1457025X-RAY DIFFRACTION99.99
5.66-49.20.16023740.17457013X-RAY DIFFRACTION99.91

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