9L5Q | pdb_00009l5q

Crystal structure of PI5P4Kalpha N251S in apo form

• PDB DOI: https://doi.org/10.2210/pdb9L5Q/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-12-23 Released: 2025-12-24 
• Deposition Author(s): Senda, M., Imai, M., Fujisaki, M., Takeuchi, K., Sasaki, A., Senda, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

A comprehensive strategy for quick determination of protein structures by MR-native SAD method

Senda, M., Senda, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.52 kDa 
• Atom Count: 2,477 
• Modeled Residue Count: 309 
• Deposited Residue Count: 453 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha	A	453	Homo sapiens	Mutation(s): 1  Gene Names: PIP4K2A, PI5P4KA, PIP5K2, PIP5K2A EC: 2.7.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for P48426 (Homo sapiens) Explore P48426  Go to UniProtKB:  P48426
PHAROS:  P48426 GTEx:  ENSG00000150867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BO3	B [auth A], C [auth A], D [auth A], E [auth A]	BORIC ACID B H3 O3 KGBXLFKZBHKPEV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.106	α = 90
b = 136.106	β = 90
c = 94.807	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Senda, M., Imai, M., Fujisaki, M., Takeuchi, K., Sasaki, A., Senda, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23am0100001

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release