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- PDB-5ain: Varenicline Interactions at the 5HT3 Receptor Ligand Binding Site... -

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Basic information

Entry
Database: PDB / ID: 5ain
TitleVarenicline Interactions at the 5HT3 Receptor Ligand Binding Site are Revealed by 5HTBP
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsSEROTONIN BINDING PROTEIN
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
VARENICLINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPrice, K.L. / Lillestol, R. / Ulens, C. / Lummis, S.C.
CitationJournal: Acs Chem Neurosci / Year: 2015
Title: Varenicline Interactions at the 5-Ht3 Receptor Ligand Binding Site are Revealed by 5-Htbp.
Authors: Price, K.L. / Lillestol, R.K. / Ulens, C. / Lummis, S.C.R.
History
DepositionFeb 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,55110
Polymers120,4955
Non-polymers1,0565
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-70.5 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.794, 72.794, 479.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.004), (-0.024, 0.725, 0.689), (-0.017, 0.689, -0.725)
Vector: 52.963, 0.539, 0.403)

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / 5HTBP


Mass: 24098.914 Da / Num. of mol.: 5 / Fragment: SEROTONIN BINDING PROTEIN, UNP RESIDUES 20-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-QMR / VARENICLINE


Mass: 211.262 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H13N3 / Comment: medication, agonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.63 Å3/Da / Density % sol: 53.31 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→48.99 Å / Num. obs: 58174 / % possible obs: 98.5 % / Observed criterion σ(I): 2.2 / Redundancy: 3.2 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR7

2br7


Resolution: 2.3→47.293 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 2943 5.1 %
Rwork0.1624 --
obs0.1655 58031 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8249 0 80 493 8822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078599
X-RAY DIFFRACTIONf_angle_d1.08211738
X-RAY DIFFRACTIONf_dihedral_angle_d14.6423150
X-RAY DIFFRACTIONf_chiral_restr0.0711315
X-RAY DIFFRACTIONf_plane_restr0.0051504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33770.29381400.23812585X-RAY DIFFRACTION98
2.3377-2.3780.26681370.23532571X-RAY DIFFRACTION100
2.378-2.42130.30591400.22952630X-RAY DIFFRACTION100
2.4213-2.46780.33481380.23152606X-RAY DIFFRACTION100
2.4678-2.51820.29121560.22312631X-RAY DIFFRACTION100
2.5182-2.5730.29691480.21762575X-RAY DIFFRACTION100
2.573-2.63280.28951410.21112629X-RAY DIFFRACTION100
2.6328-2.69860.26651610.20212605X-RAY DIFFRACTION99
2.6986-2.77160.27371230.19122597X-RAY DIFFRACTION99
2.7716-2.85310.2711520.1872585X-RAY DIFFRACTION98
2.8531-2.94520.25171460.1872632X-RAY DIFFRACTION99
2.9452-3.05050.27491700.18932618X-RAY DIFFRACTION100
3.0505-3.17260.25581370.18012643X-RAY DIFFRACTION99
3.1726-3.31690.23171260.16832683X-RAY DIFFRACTION100
3.3169-3.49170.2121340.1572632X-RAY DIFFRACTION99
3.4917-3.71040.25741230.15072642X-RAY DIFFRACTION98
3.7104-3.99680.18041520.14292623X-RAY DIFFRACTION98
3.9968-4.39870.18331360.12112614X-RAY DIFFRACTION96
4.3987-5.03460.15591260.11332615X-RAY DIFFRACTION95
5.0346-6.34070.18911260.14852663X-RAY DIFFRACTION94
6.3407-47.30290.20131310.16592709X-RAY DIFFRACTION89
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)
11.74390.11940.4230.67940.5112.4119-0.1019-0.27820.09520.18980.04570.11120.0625-0.46450.04930.30040.07870.02310.51480.11980.359110.6422-34.0689-9.5993
21.01610.08560.14332.1108-0.21142.549-0.0301-0.04220.04350.0934-0.0738-0.157-0.05450.23860.10350.18940.0816-0.02840.41190.05190.285836.0469-27.2878-14.9524
31.25940.84830.23811.4478-0.25552.6303-0.05440.1460.01350.0238-0.0855-0.2097-0.01920.40780.12640.17660.04160.00190.52880.10580.330237.8968-22.634-41.1786
42.2264-0.69940.41042.69-0.31621.9238-0.00020.26560.1185-0.08290.04220.02590.0755-0.1817-0.03210.2222-0.02180.03210.51150.07030.242113.9483-26.6338-51.8705
51.8725-0.7283-0.26651.8512-0.21712.0564-0.1079-0.1069-0.11410.08060.18590.2720.1673-0.598-0.06810.2659-0.0818-0.01920.66920.11240.3559-3.1054-33.5288-32.4358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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