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

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Basic information

Entry
Database: PDB / ID: 2xnt
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
BROMIDE ION / (2S)-2-[(4-CHLOROBENZYL)OXY]-2-PHENYLETHANAMINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 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
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)269,87630
Polymers266,46010
Non-polymers3,41720
Water00
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)134,93815
Polymers133,2305
Non-polymers1,70810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-63.2 kcal/mol
Surface area42400 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)134,93815
Polymers133,2305
Non-polymers1,70810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-63.2 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.111, 144.867, 145.106
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


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-VU2 / (2S)-2-[(4-CHLOROBENZYL)OXY]-2-PHENYLETHANAMINE


Mass: 261.747 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H16ClNO
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
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: 2.94 Å3/Da / Density % sol: 58.22 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SODIUM BROMIDE, 0.1M BIS-TRIS PROPANE PH 7.5, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.21→48.37 Å / Num. obs: 43483 / % possible obs: 96.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.9 % / Biso Wilson estimate: 85.39 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.1
Reflection shellResolution: 3.21→3.39 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.4 / % possible all: 84.9

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Processing

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

2br7


Resolution: 3.21→45.76 Å / Cor.coef. Fo:Fc: 0.8924 / Cor.coef. Fo:Fc free: 0.8771 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2195 5.08 %RANDOM
Rwork0.2159 ---
obs0.2167 43238 --
Displacement parametersBiso mean: 60.33 Å2
Baniso -1Baniso -2Baniso -3
1-10.479 Å20 Å20 Å2
2---5.8176 Å20 Å2
3----4.6614 Å2
Refine analyzeLuzzati coordinate error obs: 0.707 Å
Refinement stepCycle: LAST / Resolution: 3.21→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16360 0 190 0 16550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00716970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8423150HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7610SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes450HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2400HARMONIC5
X-RAY DIFFRACTIONt_it16780HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2240SEMIHARMONIC5
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_contact17787SEMIHARMONIC4
LS refinement shellResolution: 3.21→3.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 115 5.09 %
Rwork0.3174 2143 -
all0.3192 2258 -
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)
11.5194-0.63990.40662.0428-0.13522.1063-0.0210.17830.102-0.1599-0.04580.0385-0.2533-0.00340.0668-0.13180.01020.0209-0.0441-0.0046-0.099159.57890.356314.3045
21.5413-0.09370.39592.8431-0.28431.74580.03570.1589-0.0876-0.206-0.07730.20510.2472-0.06550.0416-0.04210.07910.0317-0.0296-0.0242-0.169957.334165.25185.2852
32.96440.5497-0.12021.5819-0.44242.1301-0.0173-0.083-0.0007-0.1034-0.01380.08280.3179-0.14550.0311-0.00830.048-0.0095-0.097-0.0355-0.089458.648448.618626.5707
42.2469-0.0108-0.22631.6265-0.29921.86280.0385-0.2232-0.07890.1489-0.08720.0399-0.00990.10660.0486-0.1294-0.0098-0.0165-0.01260.0105-0.1562.005863.176248.9876
51.7674-0.0937-0.57352.272-0.52392.19440.00820.03110.02170.092-0.0541-0.023-0.307-0.010.0459-0.0794-0.0775-0.0275-0.066-0.0744-0.134562.073889.103741.166
63.150.4845-0.00942.0247-0.2041.80770.0032-0.0247-0.0752-0.0709-0.06610.06960.2165-0.09690.0629-0.0656-0.02440.0204-0.1171-0.0335-0.1037124.27634.240527.5167
71.85930.26630.11651.6806-0.17262.10670.0167-0.2513-0.01740.2967-0.04730.03610.0782-0.00290.0306-0.1182-0.04480.0084-0.07460.002-0.1487126.75550.362248.927
81.9122-0.3755-0.38671.6667-0.00932.13480.0090.08890.07290.0797-0.0999-0.0538-0.2922-0.04410.0909-0.0882-0.0654-0.0095-0.061-0.0431-0.1044125.49875.692439.7986
91.87830.13280.34652.98520.14462.05470.01760.16-0.0351-0.2614-0.06760.2010.1068-0.07790.050.01110.03150.0226-0.0236-0.0095-0.18121.73649.66465.4503
101.8646-0.09510.29421.81730.23572.2753-0.01590.16540.1997-0.12-0.0879-0.0224-0.2155-0.12740.1038-0.02420.01050.0448-0.06340.0323-0.1098122.68275.386712.9062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1 - A205, A301 - A301)
2X-RAY DIFFRACTION2(B1 - B205, B301 - B301)
3X-RAY DIFFRACTION3(C1 - C205, C301 - C301)
4X-RAY DIFFRACTION4(D1 - D205, D301 - D301)
5X-RAY DIFFRACTION5(E1 - E205, E301 - E301)
6X-RAY DIFFRACTION6(F1 - F205, F301 - F301)
7X-RAY DIFFRACTION7(G1 - G205, G301 - G301)
8X-RAY DIFFRACTION8(H1 - H205, H301 - H301)
9X-RAY DIFFRACTION9(I1 - I205, I301 - I301)
10X-RAY DIFFRACTION10(J1 - J205, J301 - J301)

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