9J4P | pdb_00009j4p

Regulatory domain and kinase domain of ALPK1 protein

• PDB DOI: https://doi.org/10.2210/pdb9J4P/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-09 Released: 2025-07-30 
• Deposition Author(s): Xu, C., Xu, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Regulatory domain and kinase domain of ALPK1 protein

Xu, C., Xu, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 82.38 kDa 
• Atom Count: 5,697 
• Modeled Residue Count: 682 
• Deposited Residue Count: 721 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-protein kinase 1	A [auth B]	446	Homo sapiens	Mutation(s): 0  Gene Names: ALPK1, KIAA1527, LAK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens) Explore Q96QP1  Go to UniProtKB:  Q96QP1
PHAROS:  Q96QP1 GTEx:  ENSG00000073331

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-protein kinase 1	B [auth A]	275	Mus musculus	Mutation(s): 0  Gene Names: Alpk1, Kiaa1527 EC: 2.7.11.1
UniProt
Find proteins for Q9CXB8 (Mus musculus) Explore Q9CXB8  Go to UniProtKB:  Q9CXB8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DY0 (Subject of Investigation/LOI)	C [auth B]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate C17 H27 N5 O16 P2 KMSFWBYFWSKGGR-FQBROAFUSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.383	α = 90
b = 93.383	β = 90
c = 172.27	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Xu, C., Xu, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release