9HHM | pdb_00009hhm

Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with HH5129

PDB DOI: https://doi.org/10.2210/pdb9HHM/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Tequatrovirus T4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-22 Released: 2025-12-03
Deposition Author(s): Klima, M., Boura, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with HH5129

Klima, M., Boura, E.

To be published.

Macromolecule Content

Total Structure Weight: 120.56 kDa
Atom Count: 7,458
Modeled Residue Count: 897
Deposited Residue Count: 1,034
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase type 2-beta,Endolysin	A, B	517	Homo sapiens, Tequatrovirus T4	Mutation(s): 0 Gene Names: PI4K2B EC: 2.7.1.67 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Find proteins for Q8TCG2 (Homo sapiens) Explore Q8TCG2 Go to UniProtKB: Q8TCG2
PHAROS: Q8TCG2 GTEx: ENSG00000038210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P00720 Q8TCG2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IVA (Subject of Investigation/LOI) Query on A1IVA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(1~{S},2~{S},4~{S},5~{R})-6-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]methyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxycyclohexane-1,2,3,4,5-pentol C₁₇ H₂₅ N₅ O₁₇ P₃ SXKKMVQPOLWBJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.24	α = 90
b = 105.24	β = 90
c = 211.64	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-03
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.