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

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Basic information

Entry
Database: PDB / ID: 1zgb
TitleCrystal Structure of Torpedo Californica Acetylcholinesterase in Complex With an (R)-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-A1E / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: NAT.STRUCT.BIOL. / Year: 1997
Title: Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A
Authors: Raves, M.L. / Harel, M. / Pang, Y.-P. / Silman, I. / Kozikowski, A.P. / 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 16, 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

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2684
Polymers61,3251
Non-polymers9433
Water3,207178
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5368
Polymers122,6502
Non-polymers1,8866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
Unit cell
Length a, b, c (Å)111.449, 111.449, 137.095
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: 61325.090 Da / Num. of mol.: 1 / 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.: 2 / 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-A1E / (5R)-5-{[10-(1,2,3,4-TETRAHYDROACRIDIN-9-YLAMINO)DECYL]AMINO}-5,6,7,8-TETRAHYDROQUINOLIN-2(1H)-ONE / (R)-N-9 -(1 ,2 ,3 ,4 -TETRAHYDROACRIDINYL)-N'-5 -[5 ,6 ,7 ,8 -TETRAHYDRO-2'(1'H)-QUINOLINONYL]-1,10-DIAMINODECANE / (R)-TACRINE(10)-HUPYRIDONE


Mass: 500.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H44N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 4.07 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 277 K
Details: PEG 200, pH 5.8, temperature 277K, VAPOR DIFFUSION, HANGING DROP. PROTEIN WAS CRYSTALLISED FROM 28% V/V PEG 200 0.5 M MES PH 5.8 AT 277K, SEEDING WITH TRIGONAL MICROCRYSTALS; THEN SOAKED IN ...Details: PEG 200, pH 5.8, temperature 277K, VAPOR DIFFUSION, HANGING DROP. PROTEIN WAS CRYSTALLISED FROM 28% V/V PEG 200 0.5 M MES PH 5.8 AT 277K, SEEDING WITH TRIGONAL MICROCRYSTALS; THEN SOAKED IN MOTHER LIQUOR (40% V/V PEG 200 IN 0.1 M MES BUFFER, PH 5.8) CONTAINING 2 MM (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 17 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: Sep 7, 2000 / 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: 2.3→30 Å / Num. obs: 44250 / % possible obs: 98.5 % / Redundancy: 1.59 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.16 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
STRATEGYdata reduction
CCP4(TRUNCATE)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.19 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1962219.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2190 5 %RANDOM
Rwork0.188 ---
obs0.188 43555 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.49 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.66 Å25.56 Å20 Å2
2--7.66 Å20 Å2
3----15.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 65 178 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.116
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2671.5
X-RAY DIFFRACTIONc_mcangle_it1.9592
X-RAY DIFFRACTIONc_scbond_it2.1692
X-RAY DIFFRACTIONc_scangle_it3.0282.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 315 4.4 %
Rwork0.218 6902 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ARE.PARARE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM

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