4ZK4 | pdb_00004zk4

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 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane

PDB DOI: https://doi.org/10.2210/pdb4ZK4/pdb

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

Deposited: 2015-04-29 Released: 2015-05-13
Deposition Author(s): Bobango, J., Wu, J., Talley, T.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.212 (Depositor), 0.213 (DCC)
R-Value Work:
0.181 (Depositor), 0.185 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Models: 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

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 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane.

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

To be published.

Macromolecule Content

Total Structure Weight: 132.27 kDa
Atom Count: 8,496
Modeled Residue Count: 1,034
Deposited Residue Count: 1,145
Unique protein chains: 1

Macromolecules

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| 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	229	Aplysia californica, Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P32297 (Homo sapiens) Explore P32297 Go to UniProtKB: P32297
PHAROS: P32297 GTEx: ENSG00000080644
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 Groups	Q8WSF8 P32297
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TII Query on TII Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth E] MOL2 format, chain K [auth C] MOL2 format, chain N [auth E] mmCIF format, chain K [auth C] mmCIF format, chain N [auth E]	K [auth C], N [auth E]	(5R)-1-methyl-7-[5-(propan-2-yloxy)pyridin-3-yl]-1,7-diazaspiro[4.4]nonane C₁₆ H₂₅ N₃ O KVSRTRCOWRKRQB-MRXNPFEDSA-N		Interactions Focus chain K [auth C] Focus chain N [auth E] Interactions & Density Focus chain K [auth C] Focus chain N [auth E]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	G [auth A], H [auth A], J [auth B], L [auth C], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth E] MOL2 format, chain F [auth A] MOL2 format, chain O [auth E] mmCIF format, chain F [auth A] mmCIF format, chain O [auth E]	F [auth A], O [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth E] Interactions & Density Focus chain F [auth A] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.212 (Depositor), 0.213 (DCC)
R-Value Work: 0.181 (Depositor), 0.185 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.662	α = 90
b = 78.205	β = 94.97
c = 120.465	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

Bobango, J.

Wu, J.

Talley, T.T.

Revision History (Full details and data files)

Version 1.0: 2015-05-13
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 1.2: 2024-10-16
Changes: Structure summary

4ZK4 | pdb_00004zk4

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 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane

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 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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