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- PDB-2xnu: Acetylcholine binding protein (AChBP) as template for hierarchica... -

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Basic information

Entry
Database: PDB / ID: 2xnu
TitleAcetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / CHOLINE-BINDING PROTEIN / IN-SILICO SCREENING / LIGAND-GATED ION CHANNELS / ELECTROPHYSIOLOGY / CYS-LOOP RECEPTORS
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
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
2-(2-(4-PHENYLPIPERIDIN-1-YL)ETHYL)-1H-INDOLE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsRucktooa, P. / Akdemir, A. / deEsch, I. / Sixma, T.K.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Acetylcholine Binding Protein (Achbp) as Template for Hierarchical in Silico Screening Procedures to Identify Structurally Novel Ligands for the Nicotinic Receptors.
Authors: Akdemir, A. / Rucktooa, P. / Jongejan, A. / Elk, R.V. / Bertrand, S. / Sixma, T.K. / Bertrand, D. / Smit, A.B. / Leurs, R. / De Graaf, C. / De Esch, I.J.
History
DepositionAug 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: 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)133,5346
Polymers133,2305
Non-polymers3041
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-65.4 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.741, 177.015, 129.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 26645.967 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: COMPOUND 6 FROM IN SILICO SCREEN
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical ChemComp-VU3 / 2-(2-(4-PHENYLPIPERIDIN-1-YL)ETHYL)-1H-INDOLE


Mass: 304.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.38 Å3/Da / Density % sol: 63.58 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SODIUM BROMIDE, 0.1M BIS-TRIS PROPANE PH 7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2833
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2008 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2833 Å / Relative weight: 1
ReflectionResolution: 2.5→40.1 Å / Num. obs: 49629 / % possible obs: 93 % / Observed criterion σ(I): 1.7 / Redundancy: 3 % / Biso Wilson estimate: 60.85 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.6 / % possible all: 91.3

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR7

2br7


Resolution: 2.55→40.09 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9025 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 2413 5.11 %RANDOM
Rwork0.2068 ---
obs0.208 47197 --
Displacement parametersBiso mean: 43.45 Å2
Baniso -1Baniso -2Baniso -3
1-3.7506 Å20 Å20 Å2
2---0.9731 Å20 Å2
3----2.7775 Å2
Refine analyzeLuzzati coordinate error obs: 0.377 Å
Refinement stepCycle: LAST / Resolution: 2.55→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8202 0 23 226 8451
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088454HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0211541HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3832SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes225HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1202HARMONIC5
X-RAY DIFFRACTIONt_it8428HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion2.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1121SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9168SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2541 148 4.27 %
Rwork0.233 3317 -
all0.234 3465 -
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)
11.14740.02670.04132.13760.64431.2772-0.038-0.03510.0759-0.11690.0423-0.0704-0.06140.0803-0.00430.13990.02030.0052-0.0283-0.01780.057264.61358.20261.201
20.90430.37350.02442.53850.4981.0946-0.05180.14630.0793-0.2180.121-0.0122-0.06660.0149-0.06920.2438-0.02010.03470.0344-0.010.040751.67663.00338.76
30.80130.13950.09243.3492-0.27050.6368-0.04350.07890.0818-0.09840.11590.3097-0.0766-0.1503-0.07230.2655-0.051-0.03880.05480.04730.084925.42760.75543.168
41.0186-0.2904-0.02571.9445-0.19521.0593-0.0225-0.16780.06230.08530.14230.1615-0.0552-0.1501-0.11990.1457-0.05020.01540.06890.0510.111122.5756.59469.992
51.1717-0.426-0.36392.25810.64321.4507-0.0981-0.19960.01350.0930.1487-0.0678-0.04170.1095-0.05070.18770.00180.00720.05960.04080.017746.93854.20380.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1 - A205)
2X-RAY DIFFRACTION2(B1 - B205)
3X-RAY DIFFRACTION3(C1 - C205)
4X-RAY DIFFRACTION4(D1 - D205)
5X-RAY DIFFRACTION5(E1 - E205)

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