[English] 日本語
Yorodumi
- PDB-4b85: Mus musculus Acetylcholinesterase in complex with 4-Chloranyl-N-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b85
TitleMus musculus Acetylcholinesterase in complex with 4-Chloranyl-N-(2- diethylamino-ethyl)-benzenesulfonamide
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / 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-B3W / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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.J. / 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 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.5Dec 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,81517
Polymers120,4682
Non-polymers2,34715
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-35.5 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.527, 112.892, 226.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 4 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.: 2
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 , 5 types, 676 molecules

#2: Chemical ChemComp-B3W / 4-chloranyl-N-[2-(diethylamino)ethyl]benzenesulfonamide


Mass: 290.809 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19ClN2O2S
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 % / 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: I911-3 / Wavelength: 1
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 Å / Relative weight: 1
ReflectionResolution: 2.1→29.2 Å / Num. obs: 119406 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 37.26 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.1→29.189 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 2414 2 %
Rwork0.1767 --
obs0.1773 119303 99.82 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.925 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-0.312 Å20 Å20 Å2
2--1.8853 Å20 Å2
3----2.1973 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 137 663 9126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088850
X-RAY DIFFRACTIONf_angle_d1.11912081
X-RAY DIFFRACTIONf_dihedral_angle_d15.8653266
X-RAY DIFFRACTIONf_chiral_restr0.0821293
X-RAY DIFFRACTIONf_plane_restr0.0051577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14290.27531510.25816767X-RAY DIFFRACTION100
2.1429-2.18940.28381490.24216800X-RAY DIFFRACTION100
2.1894-2.24030.28471570.22726771X-RAY DIFFRACTION100
2.2403-2.29640.25331470.21066832X-RAY DIFFRACTION100
2.2964-2.35840.2411480.21186817X-RAY DIFFRACTION100
2.3584-2.42780.24831370.20396832X-RAY DIFFRACTION100
2.4278-2.50610.25471070.19516869X-RAY DIFFRACTION100
2.5061-2.59560.24681560.18966819X-RAY DIFFRACTION100
2.5956-2.69950.21791460.18516851X-RAY DIFFRACTION100
2.6995-2.82220.23351410.17876874X-RAY DIFFRACTION100
2.8222-2.97090.24211350.18396857X-RAY DIFFRACTION100
2.9709-3.15680.22011500.18466881X-RAY DIFFRACTION100
3.1568-3.40020.20391310.18676894X-RAY DIFFRACTION100
3.4002-3.74180.20781410.17486954X-RAY DIFFRACTION100
3.7418-4.28180.14981400.1446945X-RAY DIFFRACTION100
4.2818-5.3890.15231370.13247041X-RAY DIFFRACTION100
5.389-29.19170.19091410.18327085X-RAY DIFFRACTION97
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)
10.6366-0.0602-0.19650.3873-0.2451.5299-0.0564-0.0543-0.04180.0322-0.0032-0.04150.11190.0823-0.00040.14260.02090.00150.10240.03160.166734.379611.247423.6276
20.3751-0.13680.5603-0.1741-0.36821.2898-0.0880.0558-0.0324-0.0709-0.01960.071-0.0867-0.2515-0.00080.25420.0088-0.01420.2418-0.01390.262118.838517.64516.7079
30.1723-0.2545-0.04110.575-0.0720.14830.04540.0205-0.3059-0.1614-0.00760.6150.3885-1.02970.02660.3256-0.20360.00660.5579-0.02180.43127.37431.202714.1137
40.1085-0.21380.2150.4726-0.28760.27020.0919-0.1045-0.0118-0.282-0.13160.17410.0873-0.144-0.01170.2755-0.0302-0.06760.4088-0.04590.289417.33816.3857-0.5931
50.1036-0.06640.08850.48840.06450.23570.08050.4036-0.1227-0.3939-0.16880.15840.003-0.178-0.0460.28610.0783-0.09190.4707-0.14650.3184-4.08685.7336-61.1897
60.20210.12820.05350.36770.52841.11180.0990.258-0.1423-0.0507-0.19180.12110.2513-0.2028-0.01610.27980.0033-0.06250.3217-0.11340.2862.43220.1139-52.7859
70.4581-0.48430.30210.55970.71531.52360.10240.1021-0.0053-0.0247-0.00980.05390.030.14710.05620.2180.0081-0.02880.2793-0.05230.247212.52995.4773-48.3994
80.9223-0.09450.40490.35910.30691.0010.22390.3140.16840.11950.0240.13440.34570.33170.16660.31090.0187-0.09040.1577-0.10020.213916.70492.699-38.5321
90.32970.16930.03660.1204-0.03570.11620.2003-0.1294-0.04850.1015-0.09520.00670.57560.0384-0.00070.5368-0.0351-0.0970.2589-0.03370.27514.1684-4.9116-17.7905
100.2156-0.3011-0.07250.42020.39340.89290.1259-0.04950.03130.169-0.17070.0955-0.0273-0.2341-00.2206-0.05280.00190.2881-0.05490.2955-2.59448.5664-32.8495
110.0552-0.053-0.11730.1940.08640.23230.0533-0.15490.1490.0878-0.01770.1955-0.2083-0.061-00.31810.00180.00590.2929-0.04950.3592-1.061422.6409-28.6634
120.0376-0.09790.0580.0318-0.04480.27610.08720.09750.10050.238-0.0940.1422-0.0210.0568-00.3673-0.02660.00210.3584-0.05530.288413.176811.708-21.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:331)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 332:486)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 487:513)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 514:542)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 4:45)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:118)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 119:275)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 276:341)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 342:406)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 407:486)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 487:513)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 514:543)

+
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