6QQP | pdb_00006qqp

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

PDB DOI: https://doi.org/10.2210/pdb6QQP/pdb

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

Deposited: 2019-02-18 Released: 2020-03-18
Deposition Author(s): Bueno, R.V., Davis, S., Dawson, A., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.210 (Depositor), 0.220 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (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: 292.33 kDa
Atom Count: 18,023
Modelled Residue Count: 2,054
Deposited Residue Count: 2,490
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WSF8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JCW (Subject of Investigation/LOI) Query on JCW Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EC [auth J] SDF format, chain GB [auth G] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain OB [auth H] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain WB [auth I] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain EC [auth J] MOL2 format, chain GB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain OB [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain WB [auth I] MOL2 format, chain ZA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain EC [auth J] mmCIF format, chain GB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain OB [auth H] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain WB [auth I] mmCIF format, chain ZA [auth F]	AA [auth C] EC [auth J] GB [auth G] JA [auth D] K [auth A] AA [auth C], EC [auth J], GB [auth G], JA [auth D], K [auth A], OB [auth H], RA [auth E], S [auth B], WB [auth I], ZA [auth F]	2-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]pyridine-4-carboxamide C₁₇ H₁₇ F N₄ O FQBYLVVJPBRDCG-OUCADQQQSA-N		Interactions Focus chain AA [auth C] Focus chain EC [auth J] Focus chain GB [auth G] Focus chain JA [auth D] Focus chain K [auth A] Focus chain OB [auth H] Focus chain RA [auth E] Focus chain S [auth B] Focus chain WB [auth I] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain EC [auth J] Focus chain GB [auth G] Focus chain JA [auth D] Focus chain K [auth A] Focus chain OB [auth H] Focus chain RA [auth E] Focus chain S [auth B] Focus chain WB [auth I] Focus chain ZA [auth F]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DC [auth I] SDF format, chain FB [auth F] SDF format, chain IA [auth C] SDF format, chain LC [auth J] SDF format, chain NB [auth G] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain VB [auth H] SDF format, chain YA [auth E] SDF format, chain Z [auth B] MOL2 format, chain DC [auth I] MOL2 format, chain FB [auth F] MOL2 format, chain IA [auth C] MOL2 format, chain LC [auth J] MOL2 format, chain NB [auth G] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain VB [auth H] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] mmCIF format, chain DC [auth I] mmCIF format, chain FB [auth F] mmCIF format, chain IA [auth C] mmCIF format, chain LC [auth J] mmCIF format, chain NB [auth G] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain VB [auth H] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B]	DC [auth I] FB [auth F] IA [auth C] LC [auth J] NB [auth G] DC [auth I], FB [auth F], IA [auth C], LC [auth J], NB [auth G], QA [auth D], R [auth A], VB [auth H], YA [auth E], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DC [auth I] Focus chain FB [auth F] Focus chain IA [auth C] Focus chain LC [auth J] Focus chain NB [auth G] Focus chain QA [auth D] Focus chain R [auth A] Focus chain VB [auth H] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain DC [auth I] Focus chain FB [auth F] Focus chain IA [auth C] Focus chain LC [auth J] Focus chain NB [auth G] Focus chain QA [auth D] Focus chain R [auth A] Focus chain VB [auth H] Focus chain YA [auth E] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain AC [auth I] SDF format, chain BA [auth C] SDF format, chain BB [auth F] SDF format, chain BC [auth I] SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain CC [auth I] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain FC [auth J] SDF format, chain GA [auth C] SDF format, chain GC [auth J] SDF format, chain HB [auth G] SDF format, chain HC [auth J] SDF format, chain IB [auth G] SDF format, chain IC [auth J] SDF format, chain JB [auth G] SDF format, chain JC [auth J] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain KC [auth J] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain PB [auth H] SDF format, chain Q [auth A] SDF format, chain QB [auth H] SDF format, chain RB [auth H] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain TB [auth H] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain UB [auth H] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain XB [auth I] SDF format, chain Y [auth B] SDF format, chain YB [auth I] SDF format, chain ZB [auth I] SDF format, chain EB [auth F] SDF format, chain HA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth D] MOL2 format, chain AB [auth F] MOL2 format, chain AC [auth I] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain BC [auth I] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain CC [auth I] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain GC [auth J] MOL2 format, chain HB [auth G] MOL2 format, chain HC [auth J] MOL2 format, chain IB [auth G] MOL2 format, chain IC [auth J] MOL2 format, chain JB [auth G] MOL2 format, chain JC [auth J] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain KC [auth J] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth H] MOL2 format, chain RB [auth H] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth H] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth H] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain XB [auth I] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth I] MOL2 format, chain ZB [auth I] MOL2 format, chain EB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] mmCIF format, chain AB [auth F] mmCIF format, chain AC [auth I] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain BC [auth I] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain CC [auth I] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain GC [auth J] mmCIF format, chain HB [auth G] mmCIF format, chain HC [auth J] mmCIF format, chain IB [auth G] mmCIF format, chain IC [auth J] mmCIF format, chain JB [auth G] mmCIF format, chain JC [auth J] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain KC [auth J] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth H] mmCIF format, chain RB [auth H] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth H] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth H] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain UB [auth H] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain XB [auth I] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth I] mmCIF format, chain ZB [auth I] mmCIF format, chain EB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D]	AB [auth F] AC [auth I] BA [auth C] BB [auth F] BC [auth I] AB [auth F], AC [auth I], BA [auth C], BB [auth F], BC [auth I], CA [auth C], CB [auth F], CC [auth I], DA [auth C], DB [auth F], EA [auth C], EB [auth F], FA [auth C], FC [auth J], GA [auth C], GC [auth J], HA [auth C], HB [auth G], HC [auth J], IB [auth G], IC [auth J], JB [auth G], JC [auth J], KA [auth D], KB [auth G], KC [auth J], L [auth A], LA [auth D], LB [auth G], M [auth A], MA [auth D], MB [auth G], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], PB [auth H], Q [auth A], QB [auth H], RB [auth H], SA [auth E], SB [auth H], T [auth B], TA [auth E], TB [auth H], U [auth B], UA [auth E], UB [auth H], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], XA [auth E], XB [auth I], Y [auth B], YB [auth I], ZB [auth I]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain AC [auth I] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain BC [auth I] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GC [auth J] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain HC [auth J] Focus chain IB [auth G] Focus chain IC [auth J] Focus chain JB [auth G] Focus chain JC [auth J] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain KC [auth J] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth H] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain RB [auth H] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth I] Focus chain Y [auth B] Focus chain YB [auth I] Focus chain ZB [auth I] Interactions & Density Focus chain AB [auth F] Focus chain AC [auth I] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain BC [auth I] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GC [auth J] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain HC [auth J] Focus chain IB [auth G] Focus chain IC [auth J] Focus chain JB [auth G] Focus chain JC [auth J] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain KC [auth J] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth H] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain RB [auth H] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth I] Focus chain Y [auth B] Focus chain YB [auth I] Focus chain ZB [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.210 (Depositor), 0.220 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.53	α = 90
b = 136.948	β = 102.74
c = 131.552	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-03-18
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: 2024-11-20
Changes: Structure summary