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- PDB-1gpn: STRUCTURE OF ACETYLCHOLINESTERASE COMPLEXED WITH HUPERZINE B AT 2... -

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Basic information

Entry
Database: PDB / ID: 1gpn
TitleSTRUCTURE OF ACETYLCHOLINESTERASE COMPLEXED WITH HUPERZINE B AT 2.35A RESOLUTION
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / CHOLINESTERASE / HUPERZINE A / HUPERZINE B / ALZHEIMER'S DISEASE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / 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 ...Acetylcholinesterase, fish/snake / : / 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
HUPERZINE B / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDvir, H. / Harel, M. / Jiang, H.L. / Silman, I. / Sussman, J.L.
CitationJournal: Biochemistry / Year: 2002
Title: X-Ray Structures of Torpedo Californica Acetylcholinesterase Complexed with (+)-Huperzine a and (-)-Huperzine B: Structural Evidence for an Active Site Rearrangement
Authors: Dvir, H. / Jiang, H.L. / Wong, D.M. / Harel, M. / Chetrit, M. / He, X.C. / Jin, G.Y. / Yu, G.L. / Tang, X.C. / Silman, I. / Bai, D.L. / Sussman, J.L.
History
DepositionNov 7, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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 1.4Dec 13, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4354
Polymers60,7371
Non-polymers6993
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.722, 111.722, 137.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60736.516 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-558 / Source method: isolated from a natural source / Details: PURIFIED FROM THE ELECTRIC ORGAN
Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: 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
#3: Chemical ChemComp-HUB / HUPERZINE B


Mass: 256.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 66.6 % / Description: DATA WERE COLLECTED USING THE ROTATION METHOD
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop / Details: Raves, M.L., (1997) Nature Struct. Biol., 4, 57.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
138 %PEG2001reservoir
20.1 MMES1reservoir
312 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: BRUKER-AXS / Detector: CCD / Date: May 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 41627 / % possible obs: 98.3 % / Redundancy: 15.9 % / Biso Wilson estimate: 44.255 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 16 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.6 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. all: 50834 / Num. measured all: 159761
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EA5

1ea5


Resolution: 2.35→20 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 2045 4.9 %RANDOM
Rwork0.1862 ---
obs0.1862 40834 98 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.116 Å2-5.513 Å20 Å2
2---9.116 Å20 Å2
3---18.233 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 47 289 4470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.529
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4HUPB.PARHUPB.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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