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- PDB-2pgz: Crystal structure of Cocaine bound to an ACh-Binding Protein -

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Basic information

Entry
Database: PDB / ID: 2pgz
TitleCrystal structure of Cocaine bound to an ACh-Binding Protein
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / non-competitive inhibitors / nicotinic acetycholine receptors / acetycholine-binding protein / benzodiazepine / galanthamine / cocaine / CHOLINE BINDING PROTEIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / 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
COCAINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHansen, S.B. / Taylor, P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Galanthamine and non-competitive inhibitor binding to ACh-binding protein: evidence for a binding site on non-alpha-subunit interfaces of heteromeric neuronal nicotinic receptors.
Authors: Hansen, S.B. / Taylor, P.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Structure summary / Category: software / struct_keywords / Item: _struct_keywords.text
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)133,38212
Polymers131,0615
Non-polymers2,3217
Water20,5551141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16710 Å2
ΔGint-27 kcal/mol
Surface area45990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.822, 115.589, 130.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Soluble acetylcholine receptor


Mass: 26212.105 Da / Num. of mol.: 5 / Fragment: residues 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Gene: synthetic
Cell line (production host): 293S N-acetylglucosaminyltransferase I deficient
Production host: Homo sapiens (human) / References: UniProt: Q8WSF8

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 1146 molecules

#3: Chemical ChemComp-COC / COCAINE / Cocaine


Mass: 303.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO4 / Comment: alkaloid*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1141 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCL 10% (w/v) PEG 400, 15% (w/v) PEG 1000, 2ul drop, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12961
22961
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONAPS 19-ID21
Detector
TypeIDDetector
ADSC QUANTUM 2101CCD
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 1.76→50 Å / Num. all: 130088 / Num. obs: 130088 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.05 / Net I/σ(I): 17.7
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.428 / % possible all: 93.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYN, Apo Aplysia AChBP

2byn


Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.615 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21018 1314 1 %RANDOM
Rwork0.17996 ---
obs0.18026 128685 99.5 %-
all-129999 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.491 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---1.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8421 0 155 1141 9717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.96812286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20851097
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57924.5440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.384151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9231555
X-RAY DIFFRACTIONr_chiral_restr0.0880.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026860
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.24024
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26186
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21016
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.55531
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22728785
X-RAY DIFFRACTIONr_scbond_it1.84933993
X-RAY DIFFRACTIONr_scangle_it2.7764.53473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 99 -
Rwork0.255 9006 -
obs--94.88 %
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)
10.5598-0.1009-0.04670.9064-0.04990.5460.0238-0.0499-0.0102-0.01440.02720.1922-0.003-0.1067-0.051-0.0854-0.00080.0049-0.0661-0.0063-0.0345-17.39165.522368.2541
20.74520.24760.20210.7369-0.10691.0707-0.0170.00250.15920.01530.00530.1205-0.1801-0.00720.0117-0.05540.0110.0023-0.1008-0.0235-0.02582.083124.351463.4665
30.5191-0.09550.04850.7471-0.06011.40070.04160.04190.103-0.0387-0.0214-0.2130.00450.2383-0.0202-0.0989-0.00570.0294-0.03170.0102-0.036526.159310.963361.9098
40.64380.1571-0.060.9230.12120.9578-0.02740.0387-0.0966-0.05110.0383-0.15540.13130.0909-0.0108-0.04560.04790.0101-0.0579-0.0182-0.063321.3022-15.772366.3358
50.85220.3660.38440.76390.29021.10260.0369-0.0075-0.10090.00120.0310.02220.1351-0.0647-0.0678-0.0253-0.02-0.0082-0.0918-0.0024-0.071-5.6315-19.159570.307
68.9063-9.97972.920811.1824-3.27280.9579-0.55220.2089-0.4114-0.2289-0.0295-1.0347-0.25530.20150.5818-0.0091-0.00710.0358-0.00710.04640.002-10.930421.820963.284
79.8894-1.0178-5.29152.7188-0.60855.1737-0.09770.94510.0502-0.79260.29120.61210.5118-1.868-0.193400.00060.000100.00030.0001-3.777924.801647.5131
82.0334-8.62277.203180.178-62.632649.12410.25390.65740.0677-0.8502-1.2855-1.60960.82851.5661.03160.0005-0.00020.00070.0007-0.001-0.001225.951531.46334.4077
9132.250576.7712-14.4856223.3764-35.4605119.1973-0.090.306-0.22461.0532-0.6298-0.41791.3367-1.79480.71980.0043-0.00440.00250.00620.0020.00586.0126-25.27567.8582
1015.8039-24.4823-17.451244.576731.055121.70130.0160.04190.1-0.1187-0.11270.01250.01420.08790.0968-0.00010.00040.0002-0.0003-0.00110.0011-19.9957-9.791769.472
112.42780.67370.914524.6204-1.255311.04720.14940.3676-0.5316-0.8361-0.2182-0.09960.39470.23460.0687-0.0298-0.0026-0.0501-0.0242-0.0711-0.0379-17.8643-15.38344.0605
1221.544710.04873.648213.64684.1113.2319-0.67021.054-0.6590.39580.65440.88440.8619-1.15090.0158-0.00060.0003-0.00120.0004-0.00040.0001-17.684312.674140.208
137.6022-7.09870.384514.30373.152110.90310.05490.5502-0.052-0.3629-0.37850.4141-0.1889-0.70350.3236-0.02680.00390.05120.03910.0059-0.141211.284118.720135.6612
1412.014221.4528-10.211538.317-18.03512.524-0.35630.69730.3119-0.5730.5867-0.01820.0904-0.5305-0.23040.04590.07190.1240.06840.07350.010827.5941-2.826935.8816
1555.8562-15.6199-14.010414.99548.503119.53630.49152.72330.8179-0.093-0.202-1.9748-0.66550.6139-0.28950.00040.0008-0.00020-0.0008-0.00049.5929-26.758542.5812
160.53790.01410.05460.6008-0.02680.39480.0037-0.00120.023-0.00360.00210.00280.01780.0235-0.00570.0390.00390.00260.0345-0.01820.02735.23282.547365.5829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 20729 - 216
2X-RAY DIFFRACTION2BB20 - 21329 - 222
3X-RAY DIFFRACTION3CC20 - 20729 - 216
4X-RAY DIFFRACTION4DD20 - 20729 - 216
5X-RAY DIFFRACTION5EE20 - 20729 - 216
6X-RAY DIFFRACTION6AH401
7X-RAY DIFFRACTION7BF - J402 - 403
8X-RAY DIFFRACTION8CK407
9X-RAY DIFFRACTION8CG402 - 406
10X-RAY DIFFRACTION9DI401
11X-RAY DIFFRACTION10EL403
12X-RAY DIFFRACTION11AA-5 - 174 - 26
13X-RAY DIFFRACTION12BB-5 - 154 - 24
14X-RAY DIFFRACTION13CC-4 - 195 - 28
15X-RAY DIFFRACTION14DD-8 - 171 - 26
16X-RAY DIFFRACTION15EE-5 - 154 - 24
17X-RAY DIFFRACTION16CO408 - 637

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