[English] 日本語
Yorodumi
- PDB-7dij: Falcilysin in complex with MK-4815 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dij
TitleFalcilysin in complex with MK-4815
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 / 2-(aminomethyl)-3,5-ditert-butyl-phenol / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 19, 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_distant_solvent_atoms.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.ls_number_reflns_R_work / _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 / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Falcilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,87411
Polymers135,0391
Non-polymers83410
Water18,3211017
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 area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.520, 105.830, 125.930
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

-
Components

-
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

-
Non-polymers , 7 types, 1027 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-H8F / 2-(aminomethyl)-3,5-ditert-butyl-phenol


Mass: 235.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25NO / Feature type: SUBJECT OF INVESTIGATION
#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.: 1017 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.48 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v PEG 3,350

-
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: 1.9→48.78 Å / Num. obs: 98800 / % possible obs: 99.85 % / Redundancy: 13.2 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1433 / Rpim(I) all: 0.04084 / Rrim(I) all: 0.1491 / Net I/σ(I): 15.48
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.358 / Num. unique obs: 9660 / CC1/2: 0.738 / CC star: 0.922 / Rpim(I) all: 0.3854 / % possible all: 98.83

-
Processing

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

3s5m


Resolution: 1.9→48.78 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 9493 5 %
Rwork0.1851 180413 -
obs0.1862 98768 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8841 0 52 1017 9910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919139
X-RAY DIFFRACTIONf_angle_d1.002712320
X-RAY DIFFRACTIONf_chiral_restr0.06171342
X-RAY DIFFRACTIONf_plane_restr0.00581574
X-RAY DIFFRACTIONf_dihedral_angle_d18.82573479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.44863010.41665784X-RAY DIFFRACTION95.48
1.92-1.940.37733120.3736018X-RAY DIFFRACTION99.72
1.94-1.970.27593140.26685988X-RAY DIFFRACTION100
1.97-1.990.29073200.25486104X-RAY DIFFRACTION99.98
1.99-2.020.27923100.24715979X-RAY DIFFRACTION100
2.02-2.050.26843190.24086040X-RAY DIFFRACTION99.98
2.05-2.080.26813170.24016048X-RAY DIFFRACTION99.98
2.08-2.110.25273150.22586036X-RAY DIFFRACTION99.97
2.11-2.140.25593180.2155964X-RAY DIFFRACTION99.98
2.14-2.180.2443220.20746079X-RAY DIFFRACTION99.98
2.18-2.210.23983160.20925991X-RAY DIFFRACTION100
2.21-2.250.28263180.25176048X-RAY DIFFRACTION99.75
2.25-2.30.26183090.21865915X-RAY DIFFRACTION99.55
2.3-2.340.20073170.19266062X-RAY DIFFRACTION99.95
2.34-2.390.22963240.18476050X-RAY DIFFRACTION100
2.39-2.450.21233170.18545986X-RAY DIFFRACTION100
2.45-2.510.2263200.18166036X-RAY DIFFRACTION100
2.51-2.580.22513210.18046029X-RAY DIFFRACTION99.98
2.58-2.650.20173170.17916025X-RAY DIFFRACTION100
2.65-2.740.19153110.17856036X-RAY DIFFRACTION99.98
2.74-2.840.18643180.17235994X-RAY DIFFRACTION100
2.84-2.950.20663210.17646029X-RAY DIFFRACTION99.98
2.95-3.090.173130.17235991X-RAY DIFFRACTION100
3.09-3.250.18493230.16616049X-RAY DIFFRACTION100
3.25-3.450.18043180.16096011X-RAY DIFFRACTION99.95
3.45-3.720.16893210.16016044X-RAY DIFFRACTION99.94
3.72-4.090.17863190.15426000X-RAY DIFFRACTION99.94
4.09-4.680.15543150.14656031X-RAY DIFFRACTION99.95
4.69-5.90.19943120.1726041X-RAY DIFFRACTION99.92
5.9-48.780.18913150.17996005X-RAY DIFFRACTION99.97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more