5BP0 | pdb_00005bp0

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 5-Fluoronicotine (TI-4650)

PDB DOI: https://doi.org/10.2210/pdb5BP0/pdb

Classification: ACETYLCHOLINE BINDING PROTEIN
Organism(s): Lymnaea stagnalis
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-05-27 Released: 2015-06-24
Deposition Author(s): Bobango, J., Sankaran, B., Park, J.F., Wu, J., Talley, T.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.248 (Depositor), 0.251 (DCC)
R-Value Work:
0.198 (Depositor), 0.205 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs

Bobango, J., Sankaran, B., Park, J.F., Wu, J., Talley, T.T.

To be published.

Macromolecule Content

Total Structure Weight: 251.43 kDa
Atom Count: 15,921
Modeled Residue Count: 2,022
Deposited Residue Count: 2,180
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	218	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 C
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain S [auth C] mmCIF format, chain M [auth A] mmCIF format, chain S [auth C]	M [auth A], S [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain S [auth C] Interactions & Density Focus chain M [auth A] Focus chain S [auth C]
FN1 Query on FN1 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain DA [auth J] SDF format, chain AA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain DA [auth J] MOL2 format, chain AA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain DA [auth J] mmCIF format, chain AA [auth H]	AA [auth H] DA [auth J] L [auth A] P [auth B] R [auth C] AA [auth H], DA [auth J], L [auth A], P [auth B], R [auth C], U [auth D], V [auth E], W [auth F]	5-fluoronicotine C₁₀ H₁₃ F N₂ WEACEDDYURLEPK-JTQLQIEISA-N		Interactions Focus chain AA [auth H] Focus chain DA [auth J] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Interactions & Density Focus chain AA [auth H] Focus chain DA [auth J] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain CA [auth J] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain X [auth G] SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain N [auth B] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain N [auth B] mmCIF format, chain BA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain N [auth B]	BA [auth J] CA [auth J] K [auth A] N [auth B] O [auth B] BA [auth J], CA [auth J], K [auth A], N [auth B], O [auth B], Q [auth C], T [auth D], X [auth G], Y [auth H], Z [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth J] Focus chain CA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth J] Focus chain CA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248 (Depositor), 0.251 (DCC)
R-Value Work: 0.198 (Depositor), 0.205 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.47	α = 90
b = 129.04	β = 106.28
c = 122.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-13
Changes: Structure summary