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- PDB-4qac: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 4qac
TitleX-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH 4-(4-methylpiperidin-1-yl)-6-(4-(trifluoromethyl)phenyl)pyrimidin-2-amine
ComponentsAcetylcholine-binding protein
KeywordsAcetylcholine-Binding Protein
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / synapse / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
Chem-KK3 / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKaczanowska, K. / Harel, M. / Radic, Z. / Changeux, J.-P. / Finn, M.G. / Taylor, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for cooperative interactions of substituted 2-aminopyrimidines with the acetylcholine binding protein.
Authors: Kaczanowska, K. / Harel, M. / Radic, Z. / Changeux, J.P. / Finn, M.G. / Taylor, P.
History
DepositionMay 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,76839
Polymers247,46310
Non-polymers6,30429
Water10,935607
1
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,77319
Polymers123,7325
Non-polymers3,04114
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-91 kcal/mol
Surface area42390 Å2
MethodPISA
2
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,99420
Polymers123,7325
Non-polymers3,26315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint-90 kcal/mol
Surface area42140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.061, 75.504, 149.757
Angle α, β, γ (deg.)90.00, 117.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 24746.338 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pFLAG-CMV3 / Cell line (production host): HEK293S-GNT1 / Production host: Homo sapiens (human) / References: UniProt: P58154
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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-KK3 / 4-(4-methylpiperidin-1-yl)-6-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine


Mass: 336.355 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C17H19F3N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.26 M ammonium phosphate monobasic, 35% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2013
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 17.741

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.829 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 6832 5.03 %random
Rwork0.2 ---
all0.2365 135865 --
obs0.2023 135865 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16751 0 416 607 17774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917569
X-RAY DIFFRACTIONf_angle_d1.20223954
X-RAY DIFFRACTIONf_dihedral_angle_d18.136581
X-RAY DIFFRACTIONf_chiral_restr0.0832691
X-RAY DIFFRACTIONf_plane_restr0.0053057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.30122620.2454168X-RAY DIFFRACTION97
2.1239-2.14890.28982210.23254262X-RAY DIFFRACTION97
2.1489-2.17510.28842070.23114242X-RAY DIFFRACTION97
2.1751-2.20260.27162390.22364223X-RAY DIFFRACTION97
2.2026-2.23160.31172250.24464260X-RAY DIFFRACTION97
2.2316-2.26210.33052020.28474255X-RAY DIFFRACTION97
2.2621-2.29450.31082190.25654243X-RAY DIFFRACTION98
2.2945-2.32870.2912400.22874242X-RAY DIFFRACTION98
2.3287-2.36510.30242400.22164255X-RAY DIFFRACTION98
2.3651-2.40390.30332240.2314239X-RAY DIFFRACTION98
2.4039-2.44530.28072530.22634245X-RAY DIFFRACTION98
2.4453-2.48980.29412540.22584213X-RAY DIFFRACTION98
2.4898-2.53770.31542090.23584328X-RAY DIFFRACTION98
2.5377-2.58950.34222280.23884263X-RAY DIFFRACTION98
2.5895-2.64580.28652110.22584245X-RAY DIFFRACTION98
2.6458-2.70730.30632200.23554366X-RAY DIFFRACTION98
2.7073-2.7750.29052330.22684260X-RAY DIFFRACTION98
2.775-2.850.29422100.22034303X-RAY DIFFRACTION98
2.85-2.93390.27642480.20324319X-RAY DIFFRACTION98
2.9339-3.02860.26392370.20334269X-RAY DIFFRACTION99
3.0286-3.13680.27672510.20244306X-RAY DIFFRACTION99
3.1368-3.26240.2782160.20724341X-RAY DIFFRACTION99
3.2624-3.41080.2192180.19934357X-RAY DIFFRACTION99
3.4108-3.59060.23572510.1844328X-RAY DIFFRACTION99
3.5906-3.81550.22322410.18684326X-RAY DIFFRACTION99
3.8155-4.10990.18972080.17114381X-RAY DIFFRACTION99
4.1099-4.52330.19522090.15684413X-RAY DIFFRACTION99
4.5233-5.17720.18651930.16354425X-RAY DIFFRACTION99
5.1772-6.52050.24262420.19294423X-RAY DIFFRACTION100
6.5205-49.84330.17942210.19264533X-RAY DIFFRACTION99

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