9F84 | pdb_00009f84

Structure of Choline O-acetyltransferase in complex with 1-Methyl-4-[2-(1-naphthyl)-2-(propylthio)ethyl]pyridinium at 1.9 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9F84/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-05-06 Released: 2025-05-21
Deposition Author(s): Forsgren, N., Ekstrom, F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.197 (Depositor), 0.197 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of choline O-acetyltransferase in complex with 1-Methyl-4-[2-(1-naphthyl)-2-(propylthio)ethyl]pyridinium at 1.9 Angstrom resultion.

Forsgren, N., Ekstrom, F.

To be published.

Macromolecule Content

Total Structure Weight: 68.46 kDa
Atom Count: 5,028
Modeled Residue Count: 578
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline O-acetyltransferase	A	612	Homo sapiens	Mutation(s): 7 Gene Names: CHAT EC: 2.3.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P28329 (Homo sapiens) Explore P28329 Go to UniProtKB: P28329
PHAROS: P28329 GTEx: ENSG00000070748
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28329
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IAP (Subject of Investigation/LOI) Query on A1IAP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-methyl-4-[(2S)-2-naphthalen-1-yl-2-propylsulfanyl-ethyl]-4H-pyridine C₂₁ H₂₅ N S BKPMCVBRTHNXHQ-NRFANRHFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.197 (Depositor), 0.197 (DCC)
R-Value Work: 0.168 (Depositor), 0.168 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.66	α = 90
b = 76.766	β = 90
c = 164.324	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.