[English] 日本語
Yorodumi
- PDB-6sbr: The crystal structure of PfA-M1 in complex with 7-amino-1,4-dibro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sbr
TitleThe crystal structure of PfA-M1 in complex with 7-amino-1,4-dibromo-5,7,8,9-tetrahydrobenzocyclohepten-6-one
ComponentsM1-family alanyl aminopeptidase
KeywordsHYDROLASE / M1 AMINOPEPTIDASE
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm
Similarity search - Function
Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold ...Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-L5E / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å
AuthorsSalomon, E. / Schmitt, M. / Mouray, E. / McEwen, A.G. / Torchy, M. / Poussin-Courmontagne, P. / Alavi, S. / Tarnus, C. / Cavarelli, J. / Florent, I. / Albrecht, S.
Funding support France, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BS07-0020-01 France
French National Research AgencyANR-10-INBS-05 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Aminobenzosuberone derivatives as PfA-M1 inhibitors: Molecular recognition and antiplasmodial evaluation.
Authors: Salomon, E. / Schmitt, M. / Mouray, E. / McEwen, A.G. / Bounaadja, L. / Torchy, M. / Poussin-Courmontagne, P. / Alavi, S. / Tarnus, C. / Cavarelli, J. / Florent, I. / Albrecht, S.
History
DepositionJul 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M1-family alanyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4456
Polymers107,6181
Non-polymers8275
Water22,8071266
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-8 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.161, 109.662, 113.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein M1-family alanyl aminopeptidase


Mass: 107617.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1311800 / Plasmid: pET45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IEK1, membrane alanyl aminopeptidase

-
Non-polymers , 6 types, 1271 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-L5E / [(7~{S})-1,4-bis(bromanyl)-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium


Mass: 352.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14Br2NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1266 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1M BIS-TRIS propane pH 6.5, 0.2M sodium malonate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.43→63.815 Å / Num. obs: 172697 / % possible obs: 97.6 % / Redundancy: 5.38 % / Biso Wilson estimate: 33.608 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.089 / Χ2: 1.168 / Net I/σ(I): 10.98 / Num. measured all: 929050
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.43-1.525.33611.9770.1514430328337270430.1413.26895.4
1.52-1.625.3121.8990.8313715526653258210.4932.10796.9
1.62-1.755.5530.7122.413483124905242800.8430.78697.5
1.75-1.925.2870.2915.5611803222892223230.9610.32397.5
1.92-2.155.3570.12911.8410923720793203920.9890.14398.1
2.15-2.485.4960.08119.1610008018411182080.9950.08998.9
2.48-3.045.2580.05924.998151915648155040.9970.06699.1
3.04-4.295.570.04236.226788512245121870.9980.04699.5
4.29-63.8155.1890.03538.8436008702269390.9980.03998.8

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6SBQ

6sbq


Resolution: 1.54→63.815 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.85
RfactorNum. reflection% reflection
Rfree0.181 6992 5 %
Rwork0.143 --
obs0.1449 139813 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.3 Å2 / Biso mean: 26.498 Å2 / Biso min: 12.83 Å2
Refinement stepCycle: final / Resolution: 1.54→63.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7317 0 91 1286 8694
Biso mean--37.85 37.34 -
Num. residues----891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.55750.43252270.4199426796
1.5575-1.57580.42462260.3904432597
1.5758-1.5950.37082290.3576434598
1.595-1.61520.33412280.3168433797
1.6152-1.63650.3282300.2959436097
1.6365-1.65890.30552300.2562435697
1.6589-1.68260.28832300.2295435398
1.6826-1.70770.26692290.2166435798
1.7077-1.73440.27512300.2027437298
1.7344-1.76290.24842310.1994439498
1.7629-1.79330.2572300.1922436797
1.7933-1.82590.23992310.1943438798
1.8259-1.8610.24152310.195441398
1.861-1.8990.23682300.1851436498
1.899-1.94030.1962250.1319424395
1.9403-1.98540.16592340.1318442398
1.9854-2.03510.18552320.1255443098
2.0351-2.09010.16142310.1212442799
2.0901-2.15160.16322360.1126445699
2.1516-2.2210.152330.1109443299
2.221-2.30040.15112340.1111445499
2.3004-2.39250.1722350.1154448399
2.3925-2.50140.18122370.1254447299
2.5014-2.63330.16462370.1269451099
2.6333-2.79830.16922360.1289447999
2.7983-3.01440.17672370.1294450199
3.0144-3.31770.16592410.12744560100
3.3177-3.79770.15012410.1201457299
3.7977-4.78450.13512410.1102462599
4.7845-63.8150.16662500.1616475799

+
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