[English] 日本語
Yorodumi
- PDB-6ssz: Structure of the Plasmodium falciparum falcipain 2 protease in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ssz
TitleStructure of the Plasmodium falciparum falcipain 2 protease in complex with an (E)-chalcone inhibitor.
ComponentsCysteine proteinase falcipain 2a
KeywordsHYDROLASE / Inhibitor / complex / malaria / haemoglobin / proteolysis
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-JV1 / Falcipain 2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsMachin, J. / Kantsadi, A. / Vakonakis, I.
CitationJournal: Malar.J. / Year: 2019
Title: The complex of Plasmodium falciparum falcipain-2 protease with an (E)-chalcone-based inhibitor highlights a novel, small, molecule-binding site.
Authors: Machin, J.M. / Kantsadi, A.L. / Vakonakis, I.
History
DepositionSep 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine proteinase falcipain 2a
B: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9544
Polymers54,3592
Non-polymers5952
Water00
1
A: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4772
Polymers27,1801
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4772
Polymers27,1801
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.431, 109.431, 107.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Cysteine proteinase falcipain 2a / Falcipain 2


Mass: 27179.660 Da / Num. of mol.: 2 / Mutation: C25A
Source method: isolated from a genetically manipulated source
Details: Features a C25A mutation using the numbering system of the entry.
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9N6S8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-JV1 / (~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one


Mass: 297.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11NO5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% ...Details: Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% w/v PEG 4000. Crystal soaked for 2 hours with (E)-chalcone #48 inhibitor. Inhibitor prepared in 100% DMSO, 100 mM concentration and then diluted to 1 mM in mother liquor for crystal soaking.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.45→94.77 Å / Num. obs: 6001 / % possible obs: 90.2 % / Redundancy: 18.9 % / Biso Wilson estimate: 147.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.048 / Rrim(I) all: 0.209 / Net I/σ(I): 10.7
Reflection shellResolution: 3.45→3.85 Å / Redundancy: 17.6 % / Rmerge(I) obs: 2.31 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 301 / CC1/2: 0.44 / Rpim(I) all: 0.554 / Rrim(I) all: 2.378 / % possible all: 66.9

-
Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUL

2oul


Resolution: 3.45→94.77 Å / Cross valid method: THROUGHOUT
Details: Automatically applied NCS and TLS restraints. Refined using RCSB 2OUL as external target restraint.
RfactorNum. reflection% reflectionSelection details
Rfree0.308 288 4.8 %Random selection
Rwork0.255 ---
obs0.258 5712 59.2 %-
Refinement stepCycle: LAST / Resolution: 3.45→94.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 44 0 3837

+
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