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), 0.196 (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

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.196 (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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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.