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

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Basic information

Entry
Database: PDB / ID: 5dlp
TitleAcetylcholinesterase Methylene Blue no PEG
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Inhibitor
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
3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionSep 7, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0May 12, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Jan 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

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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)64,55020
Polymers61,3251
Non-polymers3,22519
Water27015
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,10040
Polymers122,6502
Non-polymers6,44938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area10670 Å2
ΔGint-329 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.059, 111.059, 137.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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.: 1
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

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-MBT / 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / METHYLENE BLUE


Mass: 284.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N3S / Comment: medication*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 46% PEG200 (v/v) in 100 mM NaCl/1 mM MES, pH 6.5 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→96.18 Å / Num. obs: 27016 / % possible obs: 98.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.4
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W9I

2w9i
PDB Unreleased entry


Resolution: 2.7→96.18 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.738 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22378 1356 5 %RANDOM
Rwork0.19254 ---
obs0.19409 25658 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.018 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.16 Å2-0 Å2
2---0.33 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→96.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4179 0 194 15 4388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194493
X-RAY DIFFRACTIONr_bond_other_d0.0010.024035
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9876134
X-RAY DIFFRACTIONr_angle_other_deg0.73139250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20323.95200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32215667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8731522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021062
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_it1.1623.3832127
X-RAY DIFFRACTIONr_mcbond_other1.1573.3812126
X-RAY DIFFRACTIONr_mcangle_it1.9345.0752657
X-RAY DIFFRACTIONr_mcangle_other1.9355.0762658
X-RAY DIFFRACTIONr_scbond_it1.463.7752366
X-RAY DIFFRACTIONr_scbond_other1.43.682306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3465.4813388
X-RAY DIFFRACTIONr_long_range_B_refined4.6928.9935152
X-RAY DIFFRACTIONr_long_range_B_other4.69228.9925151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 84 -
Rwork0.27 1889 -
obs--98.5 %
Refinement TLS params.Method: refined / Origin x: -53.8059 Å / Origin y: 36.5123 Å / Origin z: 10.6917 Å
111213212223313233
T0.0244 Å20.0265 Å20.0022 Å2-0.1152 Å2-0.0076 Å2--0.0078 Å2
L1.3853 °20.1751 °20.1981 °2-1.4242 °20.3648 °2--2.075 °2
S-0.0061 Å °0.0922 Å °0.0539 Å °0.0446 Å °-0.0097 Å °0.0817 Å °-0.096 Å °-0.2054 Å °0.0158 Å °

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