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

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Basic information

Entry
Database: PDB / ID: 2xnv
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


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / 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
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: 2.44 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

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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
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,50420
Polymers266,46010
Non-polymers3,04410
Water11,692649
1
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,75210
Polymers133,2305
Non-polymers1,5225
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-69.5 kcal/mol
Surface area42180 Å2
MethodPISA
2
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)134,75210
Polymers133,2305
Non-polymers1,5225
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-68 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.140, 145.140, 269.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11G-2005-

HOH

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 26645.967 Da / Num. of mol.: 10
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.: 10 / Source method: obtained synthetically / Formula: C21H24N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 3.08 Å3/Da / Density % sol: 60.09 % / Description: NONE
Crystal growpH: 7 / Details: 2M SODIUM FORMATE, pH 7

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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: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2833 Å / Relative weight: 1
ReflectionResolution: 2.44→46.77 Å / Num. obs: 107280 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 58.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 98.6

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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: 2.44→47.62 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9286 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 5025 5 %RANDOM
Rwork0.1789 ---
obs0.1806 100595 --
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.6832 Å20 Å20 Å2
2--0.6832 Å20 Å2
3----1.3664 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: LAST / Resolution: 2.44→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16360 0 230 649 17239
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117049HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.123273HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7618SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes450HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2403HARMONIC5
X-RAY DIFFRACTIONt_it16789HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2251SEMIHARMONIC5
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_contact19635SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3262 312 4.67 %
Rwork0.2635 6374 -
all0.2664 6686 -
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)
12.00740.0815-0.47821.2295-0.06180.7067-0.0247-0.0659-0.271-0.0124-0.027-0.00120.18830.14060.0517-0.0810.01970.0399-0.13530.0055-0.107-13.843439.1292173.583
21.8329-0.5039-0.01542.0119-0.20440.7816-0.0364-0.11640.27660.1357-0.0136-0.2503-0.0660.08260.05-0.1522-0.01850.0239-0.17670.0081-0.0507-5.141764.4118175.183
32.3935-0.44470.07751.7424-0.25391.25570.0383-0.14210.50290.1321-0.033-0.1743-0.1351-0.0525-0.0053-0.1546-0.00670.012-0.2530.0001-0.0091-26.199680.9339174.307
41.68880.14080.06511.8974-0.12471.33650.0272-0.05110.19740.12060.00890.1625-0.0765-0.3152-0.0361-0.15470.0218-0.0259-0.10080.0029-0.1233-48.343565.8829172.347
52.0378-0.66330.23771.7698-0.34421.5283-0.0147-0.0598-0.3679-0.00820.03680.2630.0474-0.141-0.0221-0.1518-0.0448-0.0258-0.1538-0.0017-0.0881-40.699339.9772171.769
61.2139-0.1074-0.16750.81110.08931.3715-0.01050.0739-0.1064-0.01140.01480.01350.12750.0307-0.0043-0.0226-0.0264-0.0138-0.1175-0.0519-0.118827.435192.1798173.751
71.0356-0.0113-0.12771.3146-0.22611.7859-0.02830.02920.0191-0.07270.0165-0.1599-0.00340.23050.0118-0.1115-0.01960.0279-0.0667-0.0313-0.136348.4383108.704171.461
81.1265-0.21790.27661.2868-0.13071.21160.02620.08130.0711-0.0670.0239-0.062-0.10290.0454-0.0501-0.0547-0.04690.0363-0.08440.0269-0.134139.0442133.909170.634
91.1310.15510.27470.78710.36251.8657-0.03650.05440.0694-0.0983-0.01580.1571-0.1926-0.1930.0523-0.06340.0289-0.0388-0.08210.036-0.11212.3658132.855172.307
101.1025-0.146-0.09431.29380.30471.23080.02020.0187-0.1131-0.0359-0.01140.15810.1175-0.0908-0.0089-0.1005-0.0463-0.0504-0.0814-0.0017-0.0965.1919107.202174.169
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)
6X-RAY DIFFRACTION6(F1 - F205)
7X-RAY DIFFRACTION7(G1 - G205)
8X-RAY DIFFRACTION8(H1 - H205)
9X-RAY DIFFRACTION9(I1 - I205)
10X-RAY DIFFRACTION10(J1 - J205)

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