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- PDB-5e2i: Acetylcholinesterase Methylene Blue no PEG -

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Basic information

Entry
Database: PDB / ID: 5e2i
TitleAcetylcholinesterase Methylene Blue no PEG
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Inhibitor
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
DECAMETHONIUM ION / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDym, O.
CitationJournal: Protein Sci. / Year: 2016
Title: The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex.
Authors: Dym, O. / Song, W. / Felder, C. / Roth, E. / Shnyrov, V. / Ashani, Y. / Xu, Y. / Joosten, R.P. / Weiner, L. / Sussman, J.L. / Silman, I.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Apr 10, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_assembly.oligomeric_count ..._chem_comp.pdbx_synonyms / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 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)61,1076
Polymers60,1941
Non-polymers9135
Water88349
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,21412
Polymers120,3882
Non-polymers1,82610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+8/31
Buried area3390 Å2
ΔGint-2 kcal/mol
Surface area40420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.609, 112.609, 136.871
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: 60193.977 Da / Num. of mol.: 1 / Fragment: UNP residues 25-556 / 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: 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DME / DECAMETHONIUM ION


Mass: 258.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H38N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 4.16 Å3/Da / Density % sol: 70.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG200 (v/v) in 100 mM NaCl/1 mM MES, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.65→45.9 Å / Num. obs: 29664 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.02 / Net I/σ(I): 4.5
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w91

2w91


Resolution: 2.65→45.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 17.117 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22586 1496 5 %RANDOM
Rwork0.195 ---
obs0.19655 28128 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å2-0 Å2
2---0.46 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 60 49 4351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194427
X-RAY DIFFRACTIONr_bond_other_d0.0010.024101
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9536006
X-RAY DIFFRACTIONr_angle_other_deg0.75539433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86224.028211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67115704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6051524
X-RAY DIFFRACTIONr_chiral_restr0.1610.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0082.8042127
X-RAY DIFFRACTIONr_mcbond_other1.0062.8032126
X-RAY DIFFRACTIONr_mcangle_it1.7494.2052657
X-RAY DIFFRACTIONr_mcangle_other1.7494.2062658
X-RAY DIFFRACTIONr_scbond_it1.0242.9662300
X-RAY DIFFRACTIONr_scbond_other1.0242.9682301
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7664.393350
X-RAY DIFFRACTIONr_long_range_B_refined3.46722.4645042
X-RAY DIFFRACTIONr_long_range_B_other3.52822.4685038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 107 -
Rwork0.254 2051 -
obs--99.86 %
Refinement TLS params.Method: refined / Origin x: 59.021 Å / Origin y: 28.1217 Å / Origin z: 169.608 Å
111213212223313233
T0.0428 Å2-0.0589 Å2-0.0088 Å2-0.1476 Å20.0081 Å2--0.0086 Å2
L1.1122 °20.0833 °20.3313 °2-1.6967 °2-0.4501 °2--2.237 °2
S-0.1173 Å °-0.021 Å °0.0635 Å °-0.0773 Å °0.1019 Å °-0.0605 Å °-0.1564 Å °0.1356 Å °0.0154 Å °

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