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- PDB-6nth: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -

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Basic information

Entry
Database: PDB / ID: 6nth
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by (S) Stereoisomer of A-232
ComponentsAcetylcholinesterase
Keywordshydrolase/hydrolase Inhibitor / hydrolase / inhibitor / hydrolase-hydrolase Inhibitor complex
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / synapse assembly / side of membrane / laminin binding / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / amyloid-beta binding / nervous system development / retina development in camera-type eye / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / nucleus / membrane / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
Chem-L0S / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.421 Å
AuthorsBester, S.M. / Guelta, M.A. / Height, J.J. / Pegan, S.D.
CitationJournal: To Be Published
Title: Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents
Authors: Height, J.J. / Bester, S.M. / Guelta, M.A. / Bae, S.Y. / Cheung, J. / Pegan, S.D.
History
DepositionJan 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4619
Polymers118,8942
Non-polymers2,5667
Water10,575587
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4619
Polymers118,8942
Non-polymers2,5667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4560 Å2
ΔGint25 kcal/mol
Surface area38560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.646, 105.646, 324.221
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: 59447.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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
#4: Chemical ChemComp-L0S / methyl (R)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidate / A-232


Mass: 206.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19N2O2P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 4.39 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15-21% polyethylene glycol 3350 (PEG) and 0.17- 0.21M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 80880 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Net I/σ(I): 17.5
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3893 / CC1/2: 0.954 / Rpim(I) all: 0.245 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.421→41.324 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.1734 4033 4.99 %
Rwork0.1486 --
obs0.1498 80756 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.421→41.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 166 587 9025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048757
X-RAY DIFFRACTIONf_angle_d0.67211992
X-RAY DIFFRACTIONf_dihedral_angle_d4.2976968
X-RAY DIFFRACTIONf_chiral_restr0.0461303
X-RAY DIFFRACTIONf_plane_restr0.0051571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4208-2.44920.26131400.23122580X-RAY DIFFRACTION97
2.4492-2.47910.28611260.22172591X-RAY DIFFRACTION100
2.4791-2.51050.30241400.21262628X-RAY DIFFRACTION100
2.5105-2.54350.24141410.19732599X-RAY DIFFRACTION100
2.5435-2.57830.25121360.19592652X-RAY DIFFRACTION100
2.5783-2.61520.2571670.18832557X-RAY DIFFRACTION100
2.6152-2.65420.24281350.18212604X-RAY DIFFRACTION100
2.6542-2.69570.2181570.18132616X-RAY DIFFRACTION100
2.6957-2.73990.19931070.16862621X-RAY DIFFRACTION100
2.7399-2.78710.23981380.17052654X-RAY DIFFRACTION100
2.7871-2.83780.19551450.17072588X-RAY DIFFRACTION100
2.8378-2.89230.20581450.1742629X-RAY DIFFRACTION100
2.8923-2.95140.21661330.17582654X-RAY DIFFRACTION100
2.9514-3.01550.18241080.16052653X-RAY DIFFRACTION100
3.0155-3.08560.21141610.16012576X-RAY DIFFRACTION100
3.0856-3.16280.1811300.15582646X-RAY DIFFRACTION100
3.1628-3.24830.17431240.15642654X-RAY DIFFRACTION100
3.2483-3.34380.181600.15212622X-RAY DIFFRACTION100
3.3438-3.45170.1921210.15032670X-RAY DIFFRACTION100
3.4517-3.5750.1451320.15122627X-RAY DIFFRACTION100
3.575-3.7180.15881530.13992619X-RAY DIFFRACTION100
3.718-3.88710.16021200.12792701X-RAY DIFFRACTION100
3.8871-4.09190.14111420.1212625X-RAY DIFFRACTION99
4.0919-4.3480.15011480.11842661X-RAY DIFFRACTION100
4.348-4.68330.13371450.10982659X-RAY DIFFRACTION99
4.6833-5.15380.14011550.11962680X-RAY DIFFRACTION100
5.1538-5.89770.16641240.14232751X-RAY DIFFRACTION100
5.8977-7.42340.19221470.15572748X-RAY DIFFRACTION100
7.4234-41.32970.14441530.15912858X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66742.3067-0.05094.08042.2322.76270.00790.0528-0.2129-0.2396-0.1393-0.1397-0.04010.10470.06240.4245-0.0289-0.02090.56710.04450.437670.539426.309820.5421
24.0563-1.89671.94122.9701-0.92223.8089-0.19350.47060.4636-0.1257-0.0522-0.3552-0.66550.67780.28280.5874-0.2214-0.0280.60330.12280.465367.702842.39214.356
33.471.11253.0722.22790.98542.80410.06140.05050.0576-0.2684-0.1330.132-0.31680.10570.06060.56980.0143-0.03270.5355-0.00150.368651.618132.90325.2081
43.1493-1.9982-0.99437.3329-2.60342.6517-0.114-0.5234-0.04851.2320.11740.00180.0211-0.26080.04560.6083-0.12620.02440.4963-0.02380.3579-2.586435.918957.7726
52.6757-0.7779-2.91550.29751.21075.3006-0.3701-0.2985-0.30280.38660.1104-0.18891.06490.47560.27430.6021-0.0632-0.00150.4510.04250.42587.570121.261743.8628
62.99790.8403-1.1693.4793-2.08334.01880.1761-0.08750.11730.5204-0.2454-0.1999-0.28180.36180.08860.4416-0.1491-0.08030.5139-0.00560.343114.131141.388941.0155
73.7248-2.0322-1.65863.12971.1623.91280.0465-0.1443-0.05330.4044-0.10170.0510.0110.07430.06180.3502-0.12310.00710.32380.03020.30532.874335.281340.9999
80.6947-0.94240.44811.2537-0.08673.20530.1411-0.0413-0.18570.1383-0.05180.33940.2621-0.409-0.06180.331-0.10970.02490.3677-0.00870.4015-4.924732.274234.1567
94.39-1.99341.45313.5697-1.13533.3870.09880.1849-0.0935-0.1672-0.2015-0.41930.31580.54090.12420.37940.0370.0360.58140.01950.376519.403227.232724.4857
102.6433-1.6873-0.60912.0991-0.47263.04890.0660.3528-0.2753-0.0705-0.20570.32320.222-0.13960.1140.3989-0.0743-0.00030.4798-0.04770.3004-1.794737.302622.5471
111.68370.77491.07023.4316-1.14314.3228-0.01950.05290.0995-0.1927-0.16-0.2542-0.42460.57530.17040.3873-0.07440.01940.54940.07870.405412.505853.413911.887
122.63410.4366-0.41591.85280.23144.14820.1537-0.04320.30480.1893-0.17040.089-0.39980.12540.00980.3808-0.02180.02130.32740.03720.3481-0.617751.291430.8304
133.73670.27731.58673.361-0.06776.53230.0531-0.06370.24260.072-0.07040.496-0.6768-0.81990.07030.36030.08550.06970.4818-0.02530.4616-12.790652.013932.8403
142.28450.1136-1.54410.74590.62169.3665-0.20940.27140.06140.1143-0.02190.29240.1313-0.44430.16270.3285-0.0138-0.00760.38970.08320.3689-3.972249.594914.2157
155.44760.5001-1.31372.8194-0.444.5594-0.0673-0.28260.39980.25170.0033-0.3332-0.5410.50140.0390.54070.0026-0.13440.44210.04450.331666.860437.973945.9041
161.59590.41561.45960.601-0.34282.90370.0674-0.3235-0.14420.0951-0.051-0.07110.00130.0097-0.01510.3861-0.0079-0.04180.44550.09370.369558.297725.331838.9283
174.47781.15730.3682.58140.09513.5071-0.1216-0.21630.02810.06070.0245-0.0617-0.28710.21460.05790.34890.0251-0.05910.34670.03880.253959.546333.331835.2495
182.66270.9360.26541.8026-0.10442.7509-0.0261-0.17340.02220.1094-0.00310.1982-0.2339-0.47960.01320.37140.0874-0.03070.490.03140.329645.824631.446430.4895
191.55240.58660.93012.5920.68571.95710.1460.1468-0.30860.0841-0.0327-0.17020.37410.1709-0.09570.4240.0784-0.02130.433-0.01450.412455.082817.771811.9892
203.3272-1.571-0.22113.33321.63546.32390.10.2633-0.1366-0.1535-0.1301-0.09620.2786-0.0788-0.01850.44390.034-0.03710.4502-0.00780.37448.479418.79543.4765
213.6299-2.73120.39116.044-0.89083.3847-0.21690.19380.22570.14720.1243-0.2639-0.39950.17770.10610.4007-0.0689-0.06360.4243-0.00120.275758.527234.577213.6007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 441 through 466 )
2X-RAY DIFFRACTION2chain 'A' and (resid 467 through 513 )
3X-RAY DIFFRACTION3chain 'A' and (resid 514 through 542 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 32 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 86 )
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 170 )
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 237 )
9X-RAY DIFFRACTION9chain 'B' and (resid 238 through 300 )
10X-RAY DIFFRACTION10chain 'B' and (resid 301 through 341 )
11X-RAY DIFFRACTION11chain 'B' and (resid 342 through 406 )
12X-RAY DIFFRACTION12chain 'B' and (resid 407 through 466 )
13X-RAY DIFFRACTION13chain 'B' and (resid 467 through 513 )
14X-RAY DIFFRACTION14chain 'B' and (resid 514 through 542 )
15X-RAY DIFFRACTION15chain 'A' and (resid 3 through 45 )
16X-RAY DIFFRACTION16chain 'A' and (resid 46 through 86 )
17X-RAY DIFFRACTION17chain 'A' and (resid 87 through 170 )
18X-RAY DIFFRACTION18chain 'A' and (resid 171 through 324 )
19X-RAY DIFFRACTION19chain 'A' and (resid 325 through 366 )
20X-RAY DIFFRACTION20chain 'A' and (resid 367 through 406 )
21X-RAY DIFFRACTION21chain 'A' and (resid 407 through 440 )

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