PDB-6qqp: Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyri...

ID or keywords:

Entry

Database: PDB / ID: 6qqp

Title

Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (2)

Components

Soluble acetylcholine receptor

Keywords

SIGNALING PROTEIN / AChBP /

Acetylcholine

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

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Bueno, R.V. / Davis, S. / Dawson, A. / Hunter, W.N.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Interactions between 2'-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors
Authors: Bueno, R.V. / Davis, S. / Dawson, A. / Ondachi, P.W. / Carroll, F.I. / Hunter, W.N.

History

Deposition	Feb 18, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Mar 2, 2022	Group: Database references / Structure summary Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Jan 24, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qqp.cif.gz	446.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/6qqp ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qqp	HTTPS FTP

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Related structure data

Related structure data	6qkkC 6qqoC 5o87S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o87-2 6sh0-2 5oa0-d 5obg-d 6qkk-1 6sgv-1 2yme-1 6qqo-1 5oan-d 6sgv-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #71 - Nov 2005 Acetylcholine Receptor similarity (4)

Deposited unit

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

292 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

hetero molecules

defined by author
146 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

defined by author
146 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	209.530, 136.948, 131.552
Angle α, β, γ (deg.)	90.00, 102.74, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	A	A	20 - 224	20 - 224
2	1	ARG	ARG	B	B	20 - 224	20 - 224
1	2	ARG	ARG	A	A	20 - 224	20 - 224
2	2	ARG	ARG	C	C	20 - 224	20 - 224
1	3	ARG	ARG	A	A	20 - 224	20 - 224
2	3	ARG	ARG	D	D	20 - 224	20 - 224
1	4	GLU	GLU	A	A	20 - 223	20 - 223
2	4	GLU	GLU	E	E	20 - 223	20 - 223
1	5	ARG	ARG	A	A	20 - 224	20 - 224
2	5	ARG	ARG	F	F	20 - 224	20 - 224
1	6	ARG	ARG	A	A	20 - 224	20 - 224
2	6	ARG	ARG	G	G	20 - 224	20 - 224
1	7	ARG	ARG	A	A	20 - 224	20 - 224
2	7	ARG	ARG	H	H	20 - 224	20 - 224
1	8	ARG	ARG	A	A	20 - 224	20 - 224
2	8	ARG	ARG	I	I	20 - 224	20 - 224
1	9	ARG	ARG	A	A	20 - 224	20 - 224
2	9	ARG	ARG	J	J	20 - 224	20 - 224
1	10	ARG	ARG	B	B	20 - 224	20 - 224
2	10	ARG	ARG	C	C	20 - 224	20 - 224
1	11	ARG	ARG	B	B	20 - 224	20 - 224
2	11	ARG	ARG	D	D	20 - 224	20 - 224
1	12	GLU	GLU	B	B	20 - 223	20 - 223
2	12	GLU	GLU	E	E	20 - 223	20 - 223
1	13	ARG	ARG	B	B	20 - 224	20 - 224
2	13	ARG	ARG	F	F	20 - 224	20 - 224
1	14	ARG	ARG	B	B	20 - 224	20 - 224
2	14	ARG	ARG	G	G	20 - 224	20 - 224
1	15	ARG	ARG	B	B	20 - 224	20 - 224
2	15	ARG	ARG	H	H	20 - 224	20 - 224
1	16	ARG	ARG	B	B	20 - 224	20 - 224
2	16	ARG	ARG	I	I	20 - 224	20 - 224
1	17	ARG	ARG	B	B	20 - 224	20 - 224
2	17	ARG	ARG	J	J	20 - 224	20 - 224
1	18	ARG	ARG	C	C	20 - 224	20 - 224
2	18	ARG	ARG	D	D	20 - 224	20 - 224
1	19	GLU	GLU	C	C	20 - 223	20 - 223
2	19	GLU	GLU	E	E	20 - 223	20 - 223
1	20	ARG	ARG	C	C	20 - 224	20 - 224
2	20	ARG	ARG	F	F	20 - 224	20 - 224
1	21	ARG	ARG	C	C	20 - 224	20 - 224
2	21	ARG	ARG	G	G	20 - 224	20 - 224
1	22	ARG	ARG	C	C	20 - 224	20 - 224
2	22	ARG	ARG	H	H	20 - 224	20 - 224
1	23	ARG	ARG	C	C	20 - 224	20 - 224
2	23	ARG	ARG	I	I	20 - 224	20 - 224
1	24	ARG	ARG	C	C	20 - 224	20 - 224
2	24	ARG	ARG	J	J	20 - 224	20 - 224
1	25	GLU	GLU	D	D	20 - 223	20 - 223
2	25	GLU	GLU	E	E	20 - 223	20 - 223
1	26	ARG	ARG	D	D	20 - 224	20 - 224
2	26	ARG	ARG	F	F	20 - 224	20 - 224
1	27	ARG	ARG	D	D	20 - 224	20 - 224
2	27	ARG	ARG	G	G	20 - 224	20 - 224
1	28	ARG	ARG	D	D	20 - 224	20 - 224
2	28	ARG	ARG	H	H	20 - 224	20 - 224
1	29	ARG	ARG	D	D	20 - 224	20 - 224
2	29	ARG	ARG	I	I	20 - 224	20 - 224
1	30	ARG	ARG	D	D	20 - 224	20 - 224
2	30	ARG	ARG	J	J	20 - 224	20 - 224
1	31	GLU	GLU	E	E	20 - 223	20 - 223
2	31	GLU	GLU	F	F	20 - 223	20 - 223
1	32	GLU	GLU	E	E	20 - 223	20 - 223
2	32	GLU	GLU	G	G	20 - 223	20 - 223
1	33	GLU	GLU	E	E	20 - 223	20 - 223
2	33	GLU	GLU	H	H	20 - 223	20 - 223
1	34	GLU	GLU	E	E	20 - 223	20 - 223
2	34	GLU	GLU	I	I	20 - 223	20 - 223
1	35	GLU	GLU	E	E	20 - 223	20 - 223
2	35	GLU	GLU	J	J	20 - 223	20 - 223
1	36	ARG	ARG	F	F	20 - 224	20 - 224
2	36	ARG	ARG	G	G	20 - 224	20 - 224
1	37	ARG	ARG	F	F	20 - 224	20 - 224
2	37	ARG	ARG	H	H	20 - 224	20 - 224
1	38	ARG	ARG	F	F	20 - 224	20 - 224
2	38	ARG	ARG	I	I	20 - 224	20 - 224
1	39	ARG	ARG	F	F	20 - 224	20 - 224
2	39	ARG	ARG	J	J	20 - 224	20 - 224
1	40	ARG	ARG	G	G	20 - 224	20 - 224
2	40	ARG	ARG	H	H	20 - 224	20 - 224
1	41	ARG	ARG	G	G	20 - 224	20 - 224
2	41	ARG	ARG	I	I	20 - 224	20 - 224
1	42	ARG	ARG	G	G	20 - 224	20 - 224
2	42	ARG	ARG	J	J	20 - 224	20 - 224
1	43	ARG	ARG	H	H	20 - 224	20 - 224
2	43	ARG	ARG	I	I	20 - 224	20 - 224
1	44	ARG	ARG	H	H	20 - 224	20 - 224
2	44	ARG	ARG	J	J	20 - 224	20 - 224
1	45	ARG	ARG	I	I	20 - 224	20 - 224
2	45	ARG	ARG	J	J	20 - 224	20 - 224

NCS ensembles :

#1: Protein

Soluble acetylcholine receptor

Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: The sequence conflicts are because we have used the AChBP gene sequence provided in the Aplysia californica genome (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?hgsid=589127391_ ...
Source: (gene. exp.)

Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8

#2: Chemical

ChemComp-JCW / 2-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]pyridine-4-carboxamide

Mass: 312.341 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₇H₁₇FN₄O / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL /

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C₂H₆O₂

#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.: 10
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 924 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.49 Å³/Da / Density % sol: 64.77 % / Description: Block
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: Reservoir: 0.2 M NaCl, 0.1 M Phosphate/citrate pH 4.2 8% PEG 8000 Buffer: 50 mM Tris 250 mM NaCl pH 7.5 Protein concentration: 4 mg/ml Microseeded

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96858 Å / Relative weight: 1
Reflection	Resolution: 2.4→46.82 Å / Num. obs: 139199 / % possible obs: 98.7 % / Redundancy: 2.9 % / B_iso Wilson estimate: 29 Å² / CC_1/2: 0.95 / R_merge(I) obs: 0.089 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6884 / CC_1/2: 0.65 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5o87

5o87

Resolution: 2.4→46.82 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.915 / SU B: 6.257 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21003	6903	5 %	RANDOM
R_work	0.18785	-	-	-
obs	0.18893	131926	98.25 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 34.364 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.47 Å²	0 Å²	-0.22 Å²
2-	-	3.82 Å²	0 Å²
3-	-	-	-1.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→46.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16388	0	610	924	17922

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	17520
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	15555
X-RAY DIFFRACTION	r_angle_refined_deg	1.49	1.963	23864
X-RAY DIFFRACTION	r_angle_other_deg	0.919	3.001	36239
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.064	5.014	2089
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.612	24.62	803
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.479	15	2753
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.194	15	91
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	2664
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	19865
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3490
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.264	3.25	8251
X-RAY DIFFRACTION	r_mcbond_other	2.264	3.25	8252
X-RAY DIFFRACTION	r_mcangle_it	3.638	4.869	10318
X-RAY DIFFRACTION	r_mcangle_other	3.638	4.869	10318
X-RAY DIFFRACTION	r_scbond_it	3.307	3.735	9268
X-RAY DIFFRACTION	r_scbond_other	3.307	3.736	9269
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.388	5.447	13526
X-RAY DIFFRACTION	r_long_range_B_refined	7.437	38.069	18328
X-RAY DIFFRACTION	r_long_range_B_other	7.397	37.994	18226
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13098	0.03
1	2	B	13098	0.03
2	1	A	13132	0.04
2	2	C	13132	0.04
3	1	A	13122	0.03
3	2	D	13122	0.03
4	1	A	13010	0.04
4	2	E	13010	0.04
5	1	A	13180	0.03
5	2	F	13180	0.03
6	1	A	13148	0.04
6	2	G	13148	0.04
7	1	A	13102	0.04
7	2	H	13102	0.04
8	1	A	13160	0.03
8	2	I	13160	0.03
9	1	A	13146	0.03
9	2	J	13146	0.03
10	1	B	13162	0.04
10	2	C	13162	0.04
11	1	B	13134	0.04
11	2	D	13134	0.04
12	1	B	13008	0.04
12	2	E	13008	0.04
13	1	B	13164	0.03
13	2	F	13164	0.03
14	1	B	13126	0.05
14	2	G	13126	0.05
15	1	B	13054	0.04
15	2	H	13054	0.04
16	1	B	13148	0.04
16	2	I	13148	0.04
17	1	B	13144	0.03
17	2	J	13144	0.03
18	1	C	13104	0.04
18	2	D	13104	0.04
19	1	C	12986	0.04
19	2	E	12986	0.04
20	1	C	13136	0.04
20	2	F	13136	0.04
21	1	C	13116	0.05
21	2	G	13116	0.05
22	1	C	13034	0.05
22	2	H	13034	0.05
23	1	C	13128	0.04
23	2	I	13128	0.04
24	1	C	13110	0.04
24	2	J	13110	0.04
25	1	D	12998	0.04
25	2	E	12998	0.04
26	1	D	13184	0.03
26	2	F	13184	0.03
27	1	D	13148	0.04
27	2	G	13148	0.04
28	1	D	13088	0.04
28	2	H	13088	0.04
29	1	D	13196	0.03
29	2	I	13196	0.03
30	1	D	13184	0.02
30	2	J	13184	0.02
31	1	E	12990	0.04
31	2	F	12990	0.04
32	1	E	12976	0.04
32	2	G	12976	0.04
33	1	E	12938	0.04
33	2	H	12938	0.04
34	1	E	12992	0.04
34	2	I	12992	0.04
35	1	E	12988	0.04
35	2	J	12988	0.04
36	1	F	13156	0.04
36	2	G	13156	0.04
37	1	F	13110	0.04
37	2	H	13110	0.04
38	1	F	13146	0.04
38	2	I	13146	0.04
39	1	F	13192	0.02
39	2	J	13192	0.02
40	1	G	13056	0.04
40	2	H	13056	0.04
41	1	G	13160	0.04
41	2	I	13160	0.04
42	1	G	13108	0.04
42	2	J	13108	0.04
43	1	H	13158	0.04
43	2	I	13158	0.04
44	1	H	13144	0.04
44	2	J	13144	0.04
45	1	I	13124	0.04
45	2	J	13124	0.04

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	519	-
R_work	0.286	9737	-
obs	-	-	98.65 %

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