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- PDB-1zgc: Crystal Structure of Torpedo Californica Acetylcholinesterase in ... -

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Basic information

Entry
Database: PDB / ID: 1zgc
TitleCrystal Structure of Torpedo Californica Acetylcholinesterase in Complex With an (RS)-Tacrine(10)-Hupyridone Inhibitor.
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / SERINE-HYDROLASE / PROTEIN-INHIBITOR COMPLEX / ENANTIOMERIC SELECTIVITY / Israel Structural Proteomics Center / ISPC / Structural Genomics
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / 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 ...Acetylcholinesterase, fish/snake / : / 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-A2E / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHaviv, H. / Wong, D.M. / Greenblatt, H.M. / Carlier, P.R. / Pang, Y.P. / Silman, I. / Sussman, J.L. / Israel Structural Proteomics Center (ISPC)
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Crystal Packing Mediates Enantioselective Ligand Recognition at the Peripheral Site of Acetylcholinesterase
Authors: Haviv, H. / Wong, D.M. / Greenblatt, H.M. / Carlier, P.R. / Pang, Y.P. / Silman, I. / Sussman, J.L.
#1: Journal: BIOORG.MED.CHEM.LETT. / Year: 1999
Title: Potent, easily synthesized huperzine A-tacrine hybrid acetylcholinesterase inhibitors
Authors: Carlier, P.R. / Du, D.-M. / Han, Y.-F. / Liu, J. / Pang, Y.-P.
#2: Journal: J.Am.Chem.Soc. / Year: 2003
Title: Acetylcholinesterase Complexed with Bivalent Ligands Related to Huperzine A: Experimental Evidence for Species-Dependent Protein-Ligand Complementarity
Authors: Wong, D.M. / Greenblatt, H.M. / Dvir, H. / Carlier, P.R. / Han, Y.-F. / Pang, Y.-P. / Silman, I. / Sussman, J.L.
#3: Journal: J.Am.Chem.Soc. / Year: 2004
Title: The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design
Authors: Greenblatt, H.M. / Guillou, C. / Guenard, D. / Argaman, A. / Botti, S. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L.
#4: Journal: Science / Year: 1991
Title: Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I.
History
DepositionApr 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7589
Polymers122,6502
Non-polymers2,1077
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-6 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.996, 105.543, 150.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 61325.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
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.: 5 / Source method: obtained synthetically / 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-A2E / (5S)-5-{[10-(1,2,3,4-TETRAHYDROACRIDIN-9-YLAMINO)DECYL]AMINO}-5,6,7,8-TETRAHYDROQUINOLIN-2(1H)-ONE / (S)-N-9 -(1 ,2 ,3 ,4 -TETRAHYDROACRIDINYL)-N'-5 -[5 ,6 ,7 ,8 -TETRAHYDRO-2'(1'H)-QUINOLINONYL]-1,10-DIAMINODECANE / (S)-TACRINE(10)-HUPYRIDONE


Mass: 500.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H44N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 277 K
Details: PEG 200, pH 5.8, temperature 277K, VAPOR DIFFUSION, SITTING DROP. PROTEIN WAS CRYSTALLISED FROM 28-30% V/V PEG 200 0.5 M MES PH 5.8 AT 277K, WITHOUT SEEDING WITH MICROCRYSTALS; THEN SOAKED ...Details: PEG 200, pH 5.8, temperature 277K, VAPOR DIFFUSION, SITTING DROP. PROTEIN WAS CRYSTALLISED FROM 28-30% V/V PEG 200 0.5 M MES PH 5.8 AT 277K, WITHOUT SEEDING WITH MICROCRYSTALS; THEN SOAKED IN MOTHER LIQUOR (40% V/V PEG 200 IN 0.1 M MES BUFFER, PH 5.8) CONTAINING 4MM (RS)-(+/-)- TACRINE(10)-HUPYRIDONE ((5RS)-(+/-)-5-{[10-(1,2,3,4- TETRAHYDROACRIDIN-9-YLAMINO)DECYL]AMINO}5,6,7,8-TETRAHYDRO-QUINOLIN-2(1H)-ONE) BIS-OXALATE FOR 40 HOURS.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2003 / Details: OSMIC BLUE CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→34.5 Å / Num. obs: 84805 / % possible obs: 99.4 % / Redundancy: 0.61 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.83 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
STRATEGYdata reduction
CCP4(TRUNCATE)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.5 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.485 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4157 4.9 %RANDOM
Rwork0.196 ---
obs0.199 80089 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20 Å2
2--3.46 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 144 341 8854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0218774
X-RAY DIFFRACTIONr_bond_other_d0.0030.027701
X-RAY DIFFRACTIONr_angle_refined_deg2.5061.94611922
X-RAY DIFFRACTIONr_angle_other_deg1.2462.98817917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57451052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1990.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.029755
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021864
X-RAY DIFFRACTIONr_nbd_refined0.2140.21831
X-RAY DIFFRACTIONr_nbd_other0.2590.28837
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1030.24848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3510.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4061.55252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29228479
X-RAY DIFFRACTIONr_scbond_it3.61233522
X-RAY DIFFRACTIONr_scangle_it5.2374.53443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 273
Rwork0.265 5649

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