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- PDB-3zdg: Crystal Structure of Ls-AChBP complexed with carbamoylcholine ana... -

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Basic information

Entry
Database: PDB / ID: 3zdg
TitleCrystal Structure of Ls-AChBP complexed with carbamoylcholine analogue 3-(dimethylamino)butyl dimethylcarbamate (DMABC)
ComponentsACETYLCHOLINE BINDING PROTEIN
KeywordsACETYLCHOLINE-BINDING PROTEIN
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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
DI(HYDROXYETHYL)ETHER / 3-(dimethylamino)butyl dimethylcarbamate / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsUssing, C.A. / Hansen, C.P. / Petersen, J.G. / Jensen, A.A. / Rohde, L.A.H. / Ahring, P.K. / Nielsen, E.O. / Kastrup, J.S. / Gajhede, M. / Frolund, B. / Balle, T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Synthesis, Pharmacology, and Biostructural Characterization of Novel Alpha(4)Beta(2) Nicotinic Acetylcholine Receptor Agonists.
Authors: Ussing, C.A. / Hansen, C.P. / Petersen, J.G. / Jensen, A.A. / Rohde, L.A.H. / Ahring, P.K. / Nielsen, E.O. / Kastrup, J.S. / Gajhede, M. / Frolund, B. / Balle, T.
History
DepositionNov 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
K: ACETYLCHOLINE BINDING PROTEIN
L: ACETYLCHOLINE BINDING PROTEIN
M: ACETYLCHOLINE BINDING PROTEIN
N: ACETYLCHOLINE BINDING PROTEIN
O: ACETYLCHOLINE BINDING PROTEIN
P: ACETYLCHOLINE BINDING PROTEIN
Q: ACETYLCHOLINE BINDING PROTEIN
R: ACETYLCHOLINE BINDING PROTEIN
S: ACETYLCHOLINE BINDING PROTEIN
T: ACETYLCHOLINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,94565
Polymers477,25020
Non-polymers6,69545
Water36,7872042
1
K: ACETYLCHOLINE BINDING PROTEIN
L: ACETYLCHOLINE BINDING PROTEIN
M: ACETYLCHOLINE BINDING PROTEIN
N: ACETYLCHOLINE BINDING PROTEIN
O: ACETYLCHOLINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,37919
Polymers119,3135
Non-polymers2,06614
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-116.5 kcal/mol
Surface area40130 Å2
MethodPISA
2
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)120,83016
Polymers119,3135
Non-polymers1,51811
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-118.8 kcal/mol
Surface area40030 Å2
MethodPISA
3
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)120,73415
Polymers119,3135
Non-polymers1,42210
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14730 Å2
ΔGint-98.6 kcal/mol
Surface area40000 Å2
MethodPISA
4
P: ACETYLCHOLINE BINDING PROTEIN
Q: ACETYLCHOLINE BINDING PROTEIN
R: ACETYLCHOLINE BINDING PROTEIN
S: ACETYLCHOLINE BINDING PROTEIN
T: ACETYLCHOLINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,00215
Polymers119,3135
Non-polymers1,68910
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-81 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.730, 144.880, 139.030
Angle α, β, γ (deg.)90.00, 107.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
211CHAIN B AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
311CHAIN C AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
411CHAIN D AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
511CHAIN E AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
611CHAIN F AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
711CHAIN G AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
811CHAIN H AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
911CHAIN I AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1011CHAIN J AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1111CHAIN K AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1211CHAIN L AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1311CHAIN M AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1411CHAIN N AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1511CHAIN O AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1611CHAIN P AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1711CHAIN Q AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1811CHAIN R AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
1911CHAIN S AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)
2011CHAIN T AND (RESSEQ 1:155 OR RESSEQ 161:204 ) AND (NOT ELEMENT H)

NCS oper:
IDCodeMatrixVector
1given(0.947472, 0.273292, 0.166159), (-0.253578, 0.32525, 0.910994), (0.194924, -0.905276, 0.377467)-8.53011, 29.8533, 28.1943
2given(0.947472, 0.273292, 0.166159), (-0.253578, 0.32525, 0.910994), (0.194924, -0.905276, 0.377467)-8.53011, 29.8533, 28.1943

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Components

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Protein / Sugars , 2 types, 23 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein
ACETYLCHOLINE BINDING PROTEIN


Mass: 23862.523 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYMNAEA STAGNALIS (great pond snail) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P58154
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 5 types, 2084 molecules

#2: Chemical
ChemComp-XRX / 3-(dimethylamino)butyl dimethylcarbamate


Mass: 188.267 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C9H20N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2042 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE UNIPROT SEQUENCE INCLUDES THE SIGNAL PEPTIDE.

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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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS (AT PH 8.5 ), 2.0 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 18, 2010 / Details: MULTILAYER MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 2.48→37.34 Å / Num. obs: 164848 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 31.17 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UV6

1uv6


Resolution: 2.48→37.338 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 8251 5 %
Rwork0.1729 --
obs0.1753 164077 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→37.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31930 0 425 2042 34397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01433260
X-RAY DIFFRACTIONf_angle_d1.28945334
X-RAY DIFFRACTIONf_dihedral_angle_d13.64812460
X-RAY DIFFRACTIONf_chiral_restr0.0835155
X-RAY DIFFRACTIONf_plane_restr0.0055789
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1592X-RAY DIFFRACTIONPOSITIONAL
12B1592X-RAY DIFFRACTIONPOSITIONAL0.07
13C1588X-RAY DIFFRACTIONPOSITIONAL0.084
14D1597X-RAY DIFFRACTIONPOSITIONAL0.069
15E1600X-RAY DIFFRACTIONPOSITIONAL0.078
16F1597X-RAY DIFFRACTIONPOSITIONAL0.073
17G1597X-RAY DIFFRACTIONPOSITIONAL0.069
18H1600X-RAY DIFFRACTIONPOSITIONAL0.073
19I1597X-RAY DIFFRACTIONPOSITIONAL0.069
110J1600X-RAY DIFFRACTIONPOSITIONAL0.119
111K1588X-RAY DIFFRACTIONPOSITIONAL0.067
112L1597X-RAY DIFFRACTIONPOSITIONAL0.069
113M1585X-RAY DIFFRACTIONPOSITIONAL0.07
114N1586X-RAY DIFFRACTIONPOSITIONAL0.076
115O1585X-RAY DIFFRACTIONPOSITIONAL0.094
116P1597X-RAY DIFFRACTIONPOSITIONAL0.079
117Q1541X-RAY DIFFRACTIONPOSITIONAL0.075
118R1588X-RAY DIFFRACTIONPOSITIONAL0.076
119S1589X-RAY DIFFRACTIONPOSITIONAL0.07
120T1584X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.50820.28632200.20484698X-RAY DIFFRACTION90
2.5082-2.53770.25982830.19045219X-RAY DIFFRACTION100
2.5377-2.56860.27562810.19135162X-RAY DIFFRACTION100
2.5686-2.60110.30112750.19635149X-RAY DIFFRACTION100
2.6011-2.63530.27472910.20365210X-RAY DIFFRACTION100
2.6353-2.67140.26772760.19145209X-RAY DIFFRACTION100
2.6714-2.70960.25332650.18695203X-RAY DIFFRACTION100
2.7096-2.750.24292630.18675236X-RAY DIFFRACTION100
2.75-2.7930.25722880.18975195X-RAY DIFFRACTION100
2.793-2.83880.23982850.19535200X-RAY DIFFRACTION100
2.8388-2.88770.25732940.18325171X-RAY DIFFRACTION100
2.8877-2.94020.24472890.18645167X-RAY DIFFRACTION100
2.9402-2.99670.24242750.19135223X-RAY DIFFRACTION100
2.9967-3.05780.25022650.18785193X-RAY DIFFRACTION100
3.0578-3.12430.24662640.18315257X-RAY DIFFRACTION100
3.1243-3.19690.25312880.18495144X-RAY DIFFRACTION100
3.1969-3.27680.2342740.18845236X-RAY DIFFRACTION100
3.2768-3.36540.2382600.18015247X-RAY DIFFRACTION100
3.3654-3.46430.21512720.1685237X-RAY DIFFRACTION100
3.4643-3.57610.22992850.17335191X-RAY DIFFRACTION100
3.5761-3.70380.23172780.17285194X-RAY DIFFRACTION100
3.7038-3.85190.21182870.16095218X-RAY DIFFRACTION100
3.8519-4.02710.18662860.15465219X-RAY DIFFRACTION100
4.0271-4.23910.18093200.14115201X-RAY DIFFRACTION100
4.2391-4.50430.15532530.13475230X-RAY DIFFRACTION100
4.5043-4.85140.17762600.1445268X-RAY DIFFRACTION100
4.8514-5.33830.18292790.15095236X-RAY DIFFRACTION100
5.3383-6.10790.18922850.16685244X-RAY DIFFRACTION100
6.1079-7.68420.21882350.18675324X-RAY DIFFRACTION100
7.6842-37.34180.2272750.20465145X-RAY DIFFRACTION96

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