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- PDB-1w76: Orthorhombic form of Torpedo californica acetylcholinesterase (AC... -

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Basic information

Entry
Database: PDB / ID: 1w76
TitleOrthorhombic form of Torpedo californica acetylcholinesterase (AChE) complexed with bis-acting galanthamine derivative
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ALZHEIMER'S DISEASE / CHOLINESTERASE / GLYCOPROTEIN / GPI-ANCHOR / MUSCLE / NERVE / NEUROTRANSMITTER DEGRADATION / SERINE ESTERASE / SERINE HYDROLASE / SYNAPSE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / 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 / Alpha/Beta hydrolase fold ...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
(-)-GALANTHAMINE / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsGreenblatt, H.M. / Guillou, C. / Guenard, D. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L.
Citation
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.
#1: Journal: Bioorg.Med.Chem. / Year: 1998
Title: Potent Acetylcholinesterase Inhibitors: Design, Synthesis, and Structure-Activity Relationships of Bis-Interacting Ligands in the Galanthamine Series
Authors: Mary, A. / Renko, D.Z. / Guillou, C. / Thal, C.
History
DepositionAug 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)124,1108
Polymers122,6502
Non-polymers1,4606
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.223, 105.253, 150.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, -0.00714, -0.00293), (-0.00717, 0.99992, 0.01077), (0.00285, 0.01079, -0.99994)
Vector: 182.80691, 0.04906, 102.5855)

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Components

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 61325.090 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-564 / Source method: isolated from a natural source
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-Acetylglucosamine


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
#3: Chemical ChemComp-GNT / (-)-GALANTHAMINE / Galantamine


Mass: 287.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO3 / Comment: inhibitor, alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST THREE RESIDUES IN BOTH CHAINS NOT VISIBLE. LAST 8 RESIDUES IN BOTH CHAINS NOT VISIBLE. ...FIRST THREE RESIDUES IN BOTH CHAINS NOT VISIBLE. LAST 8 RESIDUES IN BOTH CHAINS NOT VISIBLE. RESIDUES 486-489 NOT VISIBLE IN CHAIN A, BUT ARE VISIBLE IN CHAIN B.

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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 Å3/Da / Density % sol: 59 % / Description: ISOMORPHOUS TO NATIVE ORTHORHOMBIC FORM
Crystal growTemperature: 277 K / Details: 35-40% W/V PEG 200, 0.1M MES PH5.8 4 DEG. CELSIUS

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGEPLATE / Detector: IMAGE PLATE / Date: Mar 19, 2001 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 63928 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→34.17 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1695038.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: PHTHALIMIDE AND LINKER GROUP NOT VISIBLE FOR INHIBITORS IN EITHER ACTIVE SITE OF ASYMMETRIC UNIT. PROTEIN RESIDUES 284-289, PART OF ACTIVE SITE, HAVE LITTLE OR NO ELECTRON DENSITY IN BOTH CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3188 5 %RANDOM
Rwork0.236 ---
obs0.236 63894 98.3 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 33.0197 Å2 / ksol: 0.3497 e/Å3
Displacement parametersBiso mean: 42.98 Å2
Baniso -1Baniso -2Baniso -3
1--10.54 Å20 Å20 Å2
2--24.61 Å20 Å2
3----14.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8238 0 98 115 8451
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it5.682
X-RAY DIFFRACTIONc_scangle_it6.252.5
LS refinement shellResolution: 2.3→2.41 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.395 431 5.5 %
Rwork0.357 7459 -
obs--98 %

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