6QKK | pdb_00006qkk

Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (1)

PDB DOI: https://doi.org/10.2210/pdb6QKK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Aplysia californica
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-01-29 Released: 2020-02-19
Deposition Author(s): Davis, S., Bueno, R.V., Dawson, A., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.228 (Depositor), 0.233 (DCC)
R-Value Work:
0.199 (Depositor), 0.204 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Interactions between 2'-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors

Bueno, R.V., Davis, S., Dawson, A., Ondachi, P.W., Carroll, F.I., Hunter, W.N.

(2022) Acta Crystallogr D Biol Crystallogr 78

DOI: https://doi.org/10.1107/S2059798322000754

Macromolecule Content

Total Structure Weight: 290.79 kDa
Atom Count: 18,102
Modeled Residue Count: 2,059
Deposited Residue Count: 2,490
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble acetylcholine receptor	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	249	Aplysia californica	Mutation(s): 0
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WSF8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D Focus chain I Focus chain J
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H92 (Subject of Investigation/LOI) Query on H92 Download:Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain IB [auth I] SDF format, chain K [auth A] SDF format, chain MA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain RB [auth J] SDF format, chain XA [auth G] SDF format, chain Y [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain IB [auth I] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth J] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain IB [auth I] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain RB [auth J] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth C]	DB [auth H] EA [auth D] IB [auth I] K [auth A] MA [auth E] DB [auth H], EA [auth D], IB [auth I], K [auth A], MA [auth E], R [auth B], RA [auth F], RB [auth J], XA [auth G], Y [auth C]	4-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]benzamide C₁₈ H₁₈ F N₃ O QGEMISSKSNIODJ-SQWLQELKSA-N		Interactions Focus chain DB [auth H] Focus chain EA [auth D] Focus chain IB [auth I] Focus chain K [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain XA [auth G] Focus chain Y [auth C] Interactions & Density Focus chain DB [auth H] Focus chain EA [auth D] Focus chain IB [auth I] Focus chain K [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain XA [auth G] Focus chain Y [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain OB [auth I] SDF format, chain P [auth A] SDF format, chain WB [auth J] MOL2 format, chain JA [auth D] MOL2 format, chain OB [auth I] MOL2 format, chain P [auth A] MOL2 format, chain WB [auth J] mmCIF format, chain JA [auth D] mmCIF format, chain OB [auth I] mmCIF format, chain P [auth A] mmCIF format, chain WB [auth J]	JA [auth D], OB [auth I], P [auth A], WB [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain JA [auth D] Focus chain OB [auth I] Focus chain P [auth A] Focus chain WB [auth J] Interactions & Density Focus chain JA [auth D] Focus chain OB [auth I] Focus chain P [auth A] Focus chain WB [auth J]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain EB [auth H] SDF format, chain FA [auth D] SDF format, chain JB [auth I] SDF format, chain L [auth A] SDF format, chain NA [auth E] SDF format, chain SA [auth F] SDF format, chain SB [auth J] SDF format, chain W [auth B] SDF format, chain Z [auth C] SDF format, chain YA [auth G] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain JB [auth I] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth J] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth G] mmCIF format, chain EB [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain JB [auth I] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain SA [auth F] mmCIF format, chain SB [auth J] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth G]	EB [auth H] FA [auth D] JB [auth I] L [auth A] NA [auth E] EB [auth H], FA [auth D], JB [auth I], L [auth A], NA [auth E], SA [auth F], SB [auth J], W [auth B], YA [auth G], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain EB [auth H] Focus chain FA [auth D] Focus chain JB [auth I] Focus chain L [auth A] Focus chain NA [auth E] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain W [auth B] Focus chain YA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain EB [auth H] Focus chain FA [auth D] Focus chain JB [auth I] Focus chain L [auth A] Focus chain NA [auth E] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain W [auth B] Focus chain YA [auth G] Focus chain Z [auth C]
OXL Query on OXL Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain DA [auth C] SDF format, chain FB [auth H] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain HA [auth D] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain KA [auth D] SDF format, chain KB [auth I] SDF format, chain LA [auth E] SDF format, chain LB [auth I] SDF format, chain M [auth A] SDF format, chain MB [auth I] SDF format, chain N [auth A] SDF format, chain NB [auth I] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain PB [auth I] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain QB [auth J] SDF format, chain S [auth B] SDF format, chain TA [auth F] SDF format, chain TB [auth J] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain UB [auth J] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain VB [auth J] SDF format, chain X [auth B] SDF format, chain ZA [auth G] SDF format, chain WA [auth F] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain FB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth I] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain PB [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth J] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain TB [auth J] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth J] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth J] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth G] MOL2 format, chain WA [auth F] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain DA [auth C] mmCIF format, chain FB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth I] mmCIF format, chain LA [auth E] mmCIF format, chain LB [auth I] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth I] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain PB [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain QB [auth J] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain TB [auth J] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain UB [auth J] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain VB [auth J] mmCIF format, chain X [auth B] mmCIF format, chain ZA [auth G] mmCIF format, chain WA [auth F] mmCIF format, chain BA [auth C]	AA [auth C] AB [auth G] BA [auth C] BB [auth G] CA [auth C] AA [auth C], AB [auth G], BA [auth C], BB [auth G], CA [auth C], CB [auth G], DA [auth C], FB [auth H], GA [auth D], GB [auth H], HA [auth D], HB [auth H], IA [auth D], KA [auth D], KB [auth I], LA [auth E], LB [auth I], M [auth A], MB [auth I], N [auth A], NB [auth I], O [auth A], OA [auth E], PA [auth E], PB [auth I], Q [auth A], QA [auth E], QB [auth J], S [auth B], TA [auth F], TB [auth J], U [auth B], UA [auth F], UB [auth J], V [auth B], VA [auth F], VB [auth J], WA [auth F], X [auth B], ZA [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain KB [auth I] Focus chain LA [auth E] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MB [auth I] Focus chain N [auth A] Focus chain NB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain QB [auth J] Focus chain S [auth B] Focus chain TA [auth F] Focus chain TB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth J] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth J] Focus chain WA [auth F] Focus chain X [auth B] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain KB [auth I] Focus chain LA [auth E] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MB [auth I] Focus chain N [auth A] Focus chain NB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain QB [auth J] Focus chain S [auth B] Focus chain TA [auth F] Focus chain TB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth J] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth J] Focus chain WA [auth F] Focus chain X [auth B] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.228 (Depositor), 0.233 (DCC)
R-Value Work: 0.199 (Depositor), 0.204 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.995	α = 90
b = 131.583	β = 102.77
c = 131.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2022-03-02
Changes: Database references, Structure summary
Version 1.3: 2024-01-24
Changes: Data collection, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary