[English] 日本語
Yorodumi
- PDB-6eqq: Human butyrylcholinesterase in complex with huprine 19 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eqq
TitleHuman butyrylcholinesterase in complex with huprine 19
ComponentsCholinesterase
KeywordsHYDROLASE / Complex / Inhibitor / huprine
Function / homology
Function and homology information


cholinesterase / cocaine metabolic process / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / negative regulation of synaptic transmission / acetylcholine catabolic process / hydrolase activity, acting on ester bonds / peptide hormone processing / acetylcholinesterase activity / nuclear envelope lumen / Synthesis of PC / Aspirin ADME / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / 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
BROMIDE ION / huprine 19 / Unknown ligand / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40000447819 Å
AuthorsNachon, F. / Brazzolotto, X. / Wandhammer, M. / Trovaslet-Leroy, M. / Rosenberry, T.L. / Macdonald, I.R. / Darvesh, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Defense France
CitationJournal: Molecules / Year: 2017
Title: Comparison of the Binding of Reversible Inhibitors to Human Butyrylcholinesterase and Acetylcholinesterase: A Crystallographic, Kinetic and Calorimetric Study.
Authors: Rosenberry, T.L. / Brazzolotto, X. / Macdonald, I.R. / Wandhammer, M. / Trovaslet-Leroy, M. / Darvesh, S. / Nachon, F.
History
DepositionOct 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,81921
Polymers59,7141
Non-polymers3,10620
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-36 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.297, 154.297, 134.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cholinesterase / Acylcholine acylhydrolase / Butyrylcholine esterase / Choline esterase II / Pseudocholinesterase


Mass: 59713.512 Da / Num. of mol.: 1 / Mutation: N17Q, N455Q, N481Q, N486Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Plasmid: pGS / Cell line (production host): CHO-K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

-
Sugars , 3 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#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.: 4
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, 223 molecules

#4: Chemical ChemComp-H19 / huprine 19


Mass: 314.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21ClN3
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES buffer, 2.1 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→57.13 Å / Num. obs: 31862 / % possible obs: 99.91 % / Redundancy: 9.5 % / Biso Wilson estimate: 46.4867618287 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09373 / Rpim(I) all: 0.03181 / Rrim(I) all: 0.0991 / Net I/σ(I): 17.14
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 3154 / CC1/2: 0.807 / Rpim(I) all: 0.3206 / Rrim(I) all: 0.9772 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0I

1p0i


Resolution: 2.40000447819→57.1280859052 Å / SU ML: 0.218521836804 / Cross valid method: FREE R-VALUE / σ(F): 1.34365534751 / Phase error: 21.4809239337
RfactorNum. reflection% reflectionSelection details
Rfree0.195683987417 1593 5.00062782521 %Random selection
Rwork0.1707807062 ---
obs0.172128929647 31856 99.9247176913 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.3772836568 Å2
Refinement stepCycle: LAST / Resolution: 2.40000447819→57.1280859052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 190 209 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003342683007984524
X-RAY DIFFRACTIONf_angle_d0.6292575231846158
X-RAY DIFFRACTIONf_chiral_restr0.0456791451711671
X-RAY DIFFRACTIONf_plane_restr0.00408965651156776
X-RAY DIFFRACTIONf_dihedral_angle_d9.754178989613604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.3135447923971430.2526011166442709X-RAY DIFFRACTION100
2.4775-2.5660.2680429525641420.2320600881222713X-RAY DIFFRACTION99.9649859944
2.566-2.66880.254123907251430.2184907705772715X-RAY DIFFRACTION99.9650227352
2.6688-2.79020.2493966278431440.204653905972720X-RAY DIFFRACTION100
2.7902-2.93730.1938619714521430.1819308228782719X-RAY DIFFRACTION99.9650716032
2.9373-3.12130.2177906450841440.17844260172737X-RAY DIFFRACTION99.9653018737
3.1213-3.36230.2071690937041430.1775501147492736X-RAY DIFFRACTION99.9652777778
3.3623-3.70060.1973884006661440.1551213486782731X-RAY DIFFRACTION99.9652294854
3.7006-4.2360.164818613411470.1378009891142768X-RAY DIFFRACTION99.8971898561
4.236-5.33620.1445667437151470.1394196255742808X-RAY DIFFRACTION100
5.3362-57.14420.2017125648271530.1856306130182907X-RAY DIFFRACTION99.512195122
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)
12.147364007611.030015817-0.136875929283.54770738858-0.5114217100231.456287178810.01550669831670.5629712348630.145211586158-0.705040495342-0.101106558110.0452888837773-0.1377586668850.05220628930730.0684286877170.5739196828350.0963028086164-0.007154915836650.6186288878930.1231404264930.382806439778-28.094406142422.1487133586-48.123859791
20.425629648142-0.625635092482-0.9076714524641.303253355171.206483362182.155829857160.1167689490410.204709082213-0.163183002404-0.117758460544-0.2009636226290.195682728184-0.296791273177-0.6097446407310.02652655033940.4643430000770.104659789982-0.02883449677960.514750147160.1107375226680.565834643051-44.345677367124.6305262931-33.007698186
31.97352225734-0.158980857540.000110650949492.03508563782-0.7166179448412.033643887730.1106750783550.3078971985710.137683131374-0.267385923538-0.003072261289960.0417511740327-0.02510689780620.166455832818-0.08901509528020.2647527520190.0339515530144-0.04965717043890.3195860997790.02205293854150.307236159363-25.260237476717.3220763219-34.651563854
42.21859788794-0.457712330264-0.2204381230211.895062422090.02581070684581.495092954850.0221903120505-0.1531390910220.2170038020270.2036020573230.0529934410147-0.0794539613544-0.1485516971820.0884490628364-0.1012361500820.3315704171650.0111091923213-0.07436560560030.3186277653430.05534302899290.365519421236-24.48223710619.1107495803-18.1752163352
53.791566654250.9427529376252.027098653073.936824758212.719467650995.609798975370.1050149815740.194268728189-0.216838980283-0.165486048924-0.2732242205510.7574248266580.659637866414-0.8072341856520.1408558236230.463442890386-0.0129554721142-0.1372093955870.603936063528-0.02344310901530.710040504644-47.95726333352.53264498905-36.9324930386
63.40165235773-1.43006560343-0.4292543345154.92217007054-0.7111269883923.22552382959-0.134614944674-0.361471728622-0.04328080144380.6424998665530.2648497686010.316294314209-0.00205721034475-0.301838880522-0.1385372192710.4342524218210.0298035954347-0.007957362349830.4577778935580.1187998237020.403638636882-44.304411893413.1134987309-6.47356028689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 4:65
2X-RAY DIFFRACTION2chain A and resseq 66:91
3X-RAY DIFFRACTION3(chain A and resseq 92:153) or (chain A and resseq 164:231)
4X-RAY DIFFRACTION4(chain A and resseq 290:326) or (chain A and resseq 397:515)
5X-RAY DIFFRACTION5(chain A and resseq 154:163) or (chain A and resseq 232:289)
6X-RAY DIFFRACTION6(chain A and resseq 327:396) or (chain A and resseq 516:529)

+
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