[English] 日本語
Yorodumi
- PDB-4b80: Mus musculus Acetylcholinesterase in complex with N-(2-Diethylami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b80
TitleMus musculus Acetylcholinesterase in complex with N-(2-Diethylamino-ethyl)-1-(4-fluoro-phenyl)-methanesulfonamide
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / collagen binding / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A36 / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsAndersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Berg, L. / Qian, W. / Ekstrom, F. / Linusson, A.
CitationJournal: J. Med. Chem. / Year: 2013
Title: Divergent structure-activity relationships of structurally similar acetylcholinesterase inhibitors.
Authors: Andersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Berg, L. / Engdahl, C. / Qian, W. / Ekstrom, F. / Linusson, A.
History
DepositionAug 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,53424
Polymers120,4682
Non-polymers3,06622
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-39.6 kcal/mol
Surface area38440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.867, 111.543, 227.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 5 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60233.984 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 / Cell line (production host): HEK 293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 7 types, 292 molecules

#2: Chemical ChemComp-A36 / N-[2-(diethylamino)ethyl]-1-(4-fluorophenyl)methanesulfonamide


Mass: 288.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21FN2O2S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7 / Details: 27-31 % (W/V) PEG750MME, 0.1 M HEPES PH 7.0-7.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.041
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.5→29.01 Å / Num. obs: 70343 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 41.77 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.5→28.952 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML
Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED CHAIN A 259-262 AND 543-548, CHAIN B 1-3, 259-264 AND 543-548. DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING ...Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED CHAIN A 259-262 AND 543-548, CHAIN B 1-3, 259-264 AND 543-548. DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE MODELED AS ALANINES, CHAIN A 496.
RfactorNum. reflection% reflection
Rfree0.2229 1407 2 %
Rwork0.1865 --
obs0.1872 70141 99.82 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.902 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 50.02 Å2
Baniso -1Baniso -2Baniso -3
1-12.4529 Å20 Å20 Å2
2--9.1425 Å20 Å2
3----21.5955 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8356 0 198 273 8827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088835
X-RAY DIFFRACTIONf_angle_d1.08212023
X-RAY DIFFRACTIONf_dihedral_angle_d15.6633239
X-RAY DIFFRACTIONf_chiral_restr0.0781281
X-RAY DIFFRACTIONf_plane_restr0.0051566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.37421460.30386774X-RAY DIFFRACTION100
2.5893-2.69290.35441560.26566731X-RAY DIFFRACTION100
2.6929-2.81540.28981350.24656827X-RAY DIFFRACTION100
2.8154-2.96370.26451370.22666798X-RAY DIFFRACTION100
2.9637-3.14910.2431510.21596826X-RAY DIFFRACTION100
3.1491-3.39190.2771260.21256846X-RAY DIFFRACTION100
3.3919-3.73260.23551450.19426865X-RAY DIFFRACTION100
3.7326-4.27130.20581360.15066898X-RAY DIFFRACTION100
4.2713-5.37570.12731350.13126981X-RAY DIFFRACTION100
5.3757-28.95360.18371400.16977188X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0735-1.6069-1.46871.998-0.59183.1893-0.2166-0.24110.1140.48440.1999-0.04510.09180.0073-0.0460.33940.0003-0.06040.2191-0.01910.218529.879313.007441.4702
21.6416-0.1853-0.19661.3124-0.35362.1473-0.1218-0.30630.10510.21150.0329-0.2339-0.02720.08440.0910.21610.0071-0.0360.2181-0.01620.190132.395416.377329.0978
31.3790.1256-0.9140.81540.3882.70320.0036-0.0971-0.1170.1981-0.0312-0.11820.14750.08470.04930.28180.0456-0.03850.21040.05490.273231.17018.062824.4114
41.69130.68750.53751.8956-0.34582.4723-0.11320.2759-0.2727-0.110.031-0.36410.28810.440.07910.2110.10450.01310.170.02220.21343.07228.497913.4967
53.28930.45820.75621.73450.73453.1406-0.04340.2929-0.25390.1066-0.0608-0.19040.27820.18870.13310.30280.07860.05430.25480.0590.263437.22038.0429.4446
61.68050.5124-0.25872.6912-1.61683.856-0.07240.29710.2625-0.0425-0.00020.0358-0.37770.06270.07970.20630.0048-0.00110.25420.05120.305424.13522.28071.13
75.391-3.14962.0874.3593-0.54812.6216-0.01720.76320.2592-0.3621-0.1367-0.02120.0521-0.02480.11560.2558-0.0829-0.00510.27560.04530.201822.911617.9621-8.4693
82.2236-0.0177-0.08741.96410.38913.6002-0.04590.0071-0.12490.01480.03380.22570.1638-0.64110.01120.1388-0.0424-0.02820.29210.03090.269514.381513.835816.2308
94.5213-0.48682.37818.1305-0.15375.2924-0.30640.1372-0.48120.19750.2450.85370.369-1.22630.14880.3467-0.2325-0.0110.49640.06850.43156.79841.264113.9365
101.4371-1.2155-3.0712.94962.53188.2484-0.04540.0824-0.2713-0.3701-0.19060.35720.2785-0.14080.22430.3016-0.0235-0.14470.42180.04210.294817.71086.2965-1.2817
113.3718-0.1917-1.67482.33820.32093.63560.04440.54640.1255-0.2847-0.10010.2746-0.2798-0.70270.04630.37370.0662-0.08880.459-0.14090.3008-3.71126.2791-61.8686
120.7756-0.38880.18411.10960.18291.89420.29610.2483-0.1665-0.0856-0.19110.0940.6275-0.0516-0.11540.5053-0.0287-0.06790.4563-0.1080.33335.3601-4.052-53.2024
131.82260.9065-0.58060.53460.08991.61840.06270.436-0.1048-0.3241-0.23620.27290.238-0.50210.0740.30160.0803-0.11250.48-0.13980.2894-1.21815.9556-53.9505
141.3157-0.39640.14891.70950.70492.91250.09740.1009-0.1168-0.06290.0008-0.06280.26370.3387-0.0940.24130.0105-0.04180.299-0.0440.190213.90343.1834-47.9983
155.1329-2.8505-1.94871.62391.56593.4990.11740.44080.7421-0.0692-0.0528-0.4835-0.1520.3166-0.04230.2495-0.0409-0.04090.24660.00210.308918.247214.9112-40.3318
162.02261.02990.86173.39330.47942.42880.3213-0.2192-0.36820.3945-0.0608-0.01210.79950.0866-0.28430.6442-0.0011-0.0330.2720.01020.3414.0955-6.2125-22.0888
171.39270.0450.23432.6135-0.36173.27550.1478-0.1302-0.05530.2257-0.10490.20430.1429-0.3235-0.05090.2723-0.06110.01650.3338-0.09560.25290.57755.8957-29.3366
184.0471-1.306-0.78689.0608-1.15418.79630.0688-0.19510.34080.04610.15950.6287-0.4237-0.8651-0.19380.31570.01610.06940.2608-0.04420.2442-1.643422.5898-28.9922
194.7349-0.44953.79941.2398-0.80723.3032-0.09490.3311-0.03470.1805-0.0601-0.07350.0040.31390.15580.4233-0.05990.0160.4295-0.05060.178112.692411.6875-21.7216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:45)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 46:118)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 119:214)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 215:277)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 278:324)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 325:366)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 367:406)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 407:486)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 487:513)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 514:542)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 4:45)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 46:86)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 87:118)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 119:298)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 299:331)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 332:382)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 383:486)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 487:513)
19X-RAY DIFFRACTION19CHAIN B AND (RESSEQ 514:542)

+
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