5TVC

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312)

PDB DOI: https://doi.org/10.2210/pdb5TVC/pdb

Classification: ACETYLCHOLINE-BINDING PROTEIN
Organism(s): Aplysia californica, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2016-11-08 Released: 2016-11-30
Deposition Author(s): Bobango, J., Wu, J., Talley, I.T., Talley, T.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.225
R-Value Work: 0.189
R-Value Observed: 0.190

Starting Model: 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

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312)

Bobango, J., Wu, J., Talley, I.T., Talley, T.T.

To be published.

Macromolecule Content

Total Structure Weight: 133.46 kDa
Atom Count: 8,471
Modelled Residue Count: 1,020
Deposited Residue Count: 1,150
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,Neuronal acetylcholine receptor subunit alpha-3 chimera	A, B, C, D, E	230	Aplysia californica, Homo sapiens This entity is chimeric	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Find proteins for P32297 (Homo sapiens) Explore P32297 Go to UniProtKB: P32297
PHAROS: P32297 GTEx: ENSG00000080644
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q8WSF8P32297
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7LB Query on 7LB Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E]	J [auth B], L [auth C], N [auth D], P [auth E]	(E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine C₁₇ H₂₀ N₂ O MVYJEPAEKWWVOZ-OWNNVSBGSA-N		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E]	F [auth A] G [auth A] I [auth B] K [auth C] M [auth D] F [auth A], G [auth A], I [auth B], K [auth C], M [auth D], O [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.225
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.854	α = 90
b = 78.04	β = 95.03
c = 120.569	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-30
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary

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Help and Resources

5TVC

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312)

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)