7NDV | pdb_00007ndv

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001888.

PDB DOI: https://doi.org/10.2210/pdb7NDV/pdb

Classification: CHOLINE-BINDING PROTEIN
Organism(s): Lymnaea stagnalis
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-02-02 Released: 2021-04-07
Deposition Author(s): Cederfelt, D., Boronat, P., Dobritzsch, D., Hennig, S., Fitzgerald, E.A., de Esch, I.J.P., Danielson, U.H.
Funding Organization(s): Marie Sklodowska-Curie Actions, FragNET ITN

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.233 (Depositor), 0.239 (DCC)
R-Value Work:
0.205 (Depositor), 0.213 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor

Fitzgerald, E.A., Butko, M.T., Boronat, P., Cederfelt, D., Abramsson, M., Ludviksdottir, H., van Muijlwijk-Koezen, J., de Esch, I.J.P., Dobritzsch, D., Young, T., Danielson, U.H.

(2021) Rsc Advances 11: 7527-7537

Macromolecule Content

Total Structure Weight: 274.3 kDa
Atom Count: 17,801
Modeled Residue Count: 2,041
Deposited Residue Count: 2,370
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine-binding protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	237	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154 Go to UniProtKB: P58154
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58154
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain F Focus chain H
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U8Q (Subject of Investigation/LOI) Query on U8Q Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] SDF format, chain S [auth F] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain K [auth A] SDF format, chain AA [auth I] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] MOL2 format, chain S [auth F] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth I] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H] mmCIF format, chain S [auth F] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth I]	AA [auth I] K [auth A] N [auth C] P [auth D] R [auth E] AA [auth I], K [auth A], N [auth C], P [auth D], R [auth E], S [auth F], U [auth F], V [auth G], X [auth H]	4-[4-(trifluoromethyl)phenoxy]piperidine C₁₂ H₁₄ F₃ N O HRYZQEDCGWRROX-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain K [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain AA [auth I] Focus chain K [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain X [auth H]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth F] SDF format, chain Y [auth H] SDF format, chain O [auth C] SDF format, chain M [auth B] MOL2 format, chain L [auth A] MOL2 format, chain T [auth F] MOL2 format, chain Y [auth H] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] mmCIF format, chain L [auth A] mmCIF format, chain T [auth F] mmCIF format, chain Y [auth H] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B]	L [auth A], M [auth B], O [auth C], T [auth F], Y [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain T [auth F] Focus chain Y [auth H] Interactions & Density Focus chain L [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain T [auth F] Focus chain Y [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain W [auth G] SDF format, chain Z [auth H] SDF format, chain Q [auth D] MOL2 format, chain BA [auth J] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain Q [auth D] mmCIF format, chain BA [auth J] mmCIF format, chain W [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain Q [auth D]	BA [auth J], Q [auth D], W [auth G], Z [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth J] Focus chain Q [auth D] Focus chain W [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth J] Focus chain Q [auth D] Focus chain W [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.233 (Depositor), 0.239 (DCC)
R-Value Work: 0.205 (Depositor), 0.213 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.68	α = 90
b = 121.27	β = 90
c = 239.3	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Marie Sklodowska-Curie Actions, FragNET ITN	European Union	675899

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary