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- PDB-2ph9: Galanthamine bound to an ACh-binding Protein -

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Basic information

Entry
Database: PDB / ID: 2ph9
TitleGalanthamine bound to an ACh-binding Protein
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / non-competitive inhibitors / nicotinic acetylcholine receptor / acetylcholine-binding protein / benzodiazepine / galanthamine
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
(-)-GALANTHAMINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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 / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _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)132,40410
Polymers131,0615
Non-polymers1,3445
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-51 kcal/mol
Surface area46900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.950, 145.472, 143.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-302-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21B
31C
41D
51A
12A
22B
32C
42D
52E
13A
23B
33C
43D
53E
14C
24A
34E
44D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUARGARGEE200 - 208209 - 217
21LEULEUARGARGBB200 - 208209 - 217
31LEULEUARGARGCC200 - 208209 - 217
41LEULEUARGARGDD200 - 208209 - 217
51LEULEUARGARGAA200 - 208209 - 217
12ASPASPPHEPHEAA-5 - 144 - 23
22TYRTYRPHEPHEBB-7 - 142 - 23
32ASPASPPHEPHECC-5 - 144 - 23
42ASPASPPHEPHEDD-5 - 144 - 23
52ASPASPPHEPHEEE-4 - 145 - 23
13TYRTYRVALVALAA20 - 18529 - 194
23TYRTYRVALVALBB20 - 18529 - 194
33TYRTYRVALVALCC20 - 18529 - 194
43TYRTYRVALVALDD20 - 18529 - 194
53TYRTYRVALVALEE20 - 18529 - 194
14GNTGNTGNTGNTCH301
24GNTGNTGNTGNTAF301
34GNTGNTGNTGNTEJ301
44GNTGNTGNTGNTDI301

NCS ensembles :
ID
1
2
3
4

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Components

#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 gene / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-GNT / (-)-GALANTHAMINE / Galantamine


Mass: 287.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21NO3 / Comment: inhibitor, alkaloid*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, 10% (w/v) PEG-1000, 24% (v/v) isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 33957 / Num. obs: 33957 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.14 / Χ2: 1.047 / Net I/σ(I): 8.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 14.7 / Num. unique all: 3374 / Χ2: 1.136 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.306 / Cor.coef. Fo:Fc: 0.8 / Cor.coef. Io to Ic: 0.793
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

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

2byn


Resolution: 2.88→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.893 / SU B: 28.128 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1714 5.1 %RANDOM
Rwork0.205 ---
obs0.207 33817 98.8 %-
all-33957 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.971 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.98 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8527 0 97 104 8728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228942
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.97612217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33224.599424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.508151423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.6571550
X-RAY DIFFRACTIONr_chiral_restr0.0790.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026827
X-RAY DIFFRACTIONr_nbd_refined0.2250.23469
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26134
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4620.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4160.26
X-RAY DIFFRACTIONr_mcbond_it0.6291.55438
X-RAY DIFFRACTIONr_mcangle_it1.06128733
X-RAY DIFFRACTIONr_scbond_it1.40134023
X-RAY DIFFRACTIONr_scangle_it2.3964.53484
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11E83TIGHT POSITIONAL0.060.05
12B83TIGHT POSITIONAL0.120.05
13C83TIGHT POSITIONAL0.060.05
14D83TIGHT POSITIONAL0.120.05
15A83TIGHT POSITIONAL0.050.05
11E83TIGHT THERMAL0.090.5
12B83TIGHT THERMAL0.060.5
13C83TIGHT THERMAL0.060.5
14D83TIGHT THERMAL0.070.5
15A83TIGHT THERMAL0.080.5
21A148TIGHT POSITIONAL0.040.05
22B148TIGHT POSITIONAL0.040.05
23C148TIGHT POSITIONAL0.040.05
24D148TIGHT POSITIONAL0.040.05
25E148TIGHT POSITIONAL0.090.05
21A148TIGHT THERMAL0.060.5
22B148TIGHT THERMAL0.070.5
23C148TIGHT THERMAL0.060.5
24D148TIGHT THERMAL0.060.5
25E148TIGHT THERMAL0.050.5
31A1298TIGHT POSITIONAL0.050.05
32B1298TIGHT POSITIONAL0.050.05
33C1298TIGHT POSITIONAL0.050.05
34D1298TIGHT POSITIONAL0.050.05
35E1298TIGHT POSITIONAL0.050.05
31A1298TIGHT THERMAL0.090.5
32B1298TIGHT THERMAL0.080.5
33C1298TIGHT THERMAL0.080.5
34D1298TIGHT THERMAL0.080.5
35E1298TIGHT THERMAL0.080.5
41C42TIGHT POSITIONAL0.030.05
42A42TIGHT POSITIONAL0.040.05
43E42TIGHT POSITIONAL0.030.05
44D42TIGHT POSITIONAL0.030.05
41C42TIGHT THERMAL0.050.5
42A42TIGHT THERMAL0.050.5
43E42TIGHT THERMAL0.060.5
44D42TIGHT THERMAL0.060.5
LS refinement shellResolution: 2.882→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 83 -
Rwork0.256 1953 -
obs-2036 83.27 %
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)
11.5185-0.07950.28972.9221-0.2051.8309-0.06240.0106-0.06880.0060.0330.08810.1263-0.21160.0293-0.25820.01490.0301-0.0903-0.0331-0.1895.108229.450510.0114
21.88930.4729-0.4551.45510.01761.7936-0.07190.2314-0.0402-0.20450.00890.0774-0.0199-0.13090.0629-0.16080.0335-0.0063-0.11190.0281-0.191919.011834.8105-12.2117
32.24380.0872-0.09582.28390.75252.4371-0.16810.2776-0.1562-0.00090.0794-0.02260.18660.1220.0887-0.2042-0.06920.0661-0.08250.0414-0.134945.179532.5217-5.7054
41.8287-0.4839-0.2463.8451-0.37772.8953-0.1182-0.0841-0.2225-0.0401-0.0282-0.31490.27010.29070.1464-0.2206-0.0062-0.0256-0.0728-0.0126-0.121647.089226.27120.1672
52.78790.22270.04692.7331-0.0371.8654-0.08-0.2081-0.30860.09410.049-0.11130.1586-0.07410.031-0.16720.00410.0388-0.0878-0.0139-0.260222.227824.315429.9345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 209
2X-RAY DIFFRACTION2B-5 - 208
3X-RAY DIFFRACTION3C-4 - 208
4X-RAY DIFFRACTION4D-5 - 208
5X-RAY DIFFRACTION5E-4 - 208

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