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- PDB-4dbm: Aplysia californica-AChBP in complex with triazole 18 -

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Basic information

Entry
Database: PDB / ID: 4dbm
TitleAplysia californica-AChBP in complex with triazole 18
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE-BINDING PROTEIN / In situ click-chemistry / AChBP / Nicotinic / triazole / tropane / quinolinone / Cys-loop Receptor homologue
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / membrane / identical protein binding / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-0J0 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNemecz, A. / Yamauchi, J.G. / Kim, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Generation of candidate ligands for nicotinic acetylcholine receptors via in situ click chemistry with a soluble acetylcholine binding protein template.
Authors: Grimster, N.P. / Stump, B. / Fotsing, J.R. / Weide, T. / Talley, T.T. / Yamauchi, J.G. / Nemecz, A. / Kim, C. / Ho, K.Y. / Sharpless, K.B. / Taylor, P. / Fokin, V.V.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jan 31, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_atoms / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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_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.ptnr1_label_seq_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,16512
Polymers131,0615
Non-polymers3,1047
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15260 Å2
ΔGint-50 kcal/mol
Surface area43920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.338, 115.097, 131.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Soluble acetylcholine receptor / Ac-AChBP


Mass: 26212.105 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: pFLAG-CMV3 / Cell line (production host): HEK293S-Gnt1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}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 / N-Acetylglucosamine


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
#4: Chemical
ChemComp-0J0 / (3-exo)-8,8-dimethyl-3-(4-{[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]methyl}-1H-1,2,3-triazol-1-yl)-8-azoniabicyclo[3.2.1]octane


Mass: 394.490 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H28N5O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 295 K / pH: 8
Details: 0.1M Tris-HCl, 0.25M magnesium chloride, 12% (w/v) PEG 4000, 10% (v/v) glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2008
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 59275 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 28
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.556 / Num. unique all: 2805 / Rsym value: 0.473 / % possible all: 94.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
ccp4:Phasermodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4:PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79

2byn

2pgz

2byp

2byr

2bys

3c79


Resolution: 2.3→43.29 Å / SU ML: 0.38 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1939 3.39 %
Rwork0.1942 --
obs0.1962 57215 95.04 %
all-57215 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.082 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 36.15 Å2
Baniso -1Baniso -2Baniso -3
1-7.2287 Å2-0 Å2-0 Å2
2---6.7385 Å20 Å2
3----0.4902 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8357 0 220 458 9035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138879
X-RAY DIFFRACTIONf_angle_d1.18512126
X-RAY DIFFRACTIONf_dihedral_angle_d19.4843242
X-RAY DIFFRACTIONf_chiral_restr0.0851353
X-RAY DIFFRACTIONf_plane_restr0.0071536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2995-2.3570.33951260.24683429X-RAY DIFFRACTION84
2.357-2.42070.28821310.22133648X-RAY DIFFRACTION89
2.4207-2.4920.31191300.22423768X-RAY DIFFRACTION92
2.492-2.57240.29611310.23143859X-RAY DIFFRACTION94
2.5724-2.66430.30951420.22383898X-RAY DIFFRACTION95
2.6643-2.7710.36661410.21863981X-RAY DIFFRACTION96
2.771-2.8970.27361380.21744011X-RAY DIFFRACTION97
2.897-3.04970.31611420.21574067X-RAY DIFFRACTION98
3.0497-3.24080.26141420.20474077X-RAY DIFFRACTION99
3.2408-3.49090.24021440.20124135X-RAY DIFFRACTION99
3.4909-3.8420.24051270.19383644X-RAY DIFFRACTION87
3.842-4.39750.19441450.15624166X-RAY DIFFRACTION100
4.3975-5.53850.18251470.15144218X-RAY DIFFRACTION100
5.5385-43.29440.25791530.20314375X-RAY DIFFRACTION99

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