5I0N

PI4K IIalpha bound to calcium

PDB DOI: https://doi.org/10.2210/pdb5I0N/pdb

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

Deposited: 2016-02-04 Released: 2016-03-09
Deposition Author(s): Baumlova, A., Boura, E.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.258
R-Value Work: 0.219
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

PI4K IIalpha bound to calcium

Baumlova, A., Boura, E.

To be published.

Macromolecule Content

Total Structure Weight: 64.34 kDa
Atom Count: 4,228
Modelled Residue Count: 489
Deposited Residue Count: 556
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha	A	556	Homo sapiens, Tequatrovirus T4	Mutation(s): 0 Gene Names: PI4K2A, e, T4Tp126 EC: 2.7.1.67 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BTU6 (Homo sapiens) Explore Q9BTU6 Go to UniProtKB: Q9BTU6
PHAROS: Q9BTU6 GTEx: ENSG00000155252
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7 Go to UniProtKB: D9IEF7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q9BTU6D9IEF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.258
R-Value Work: 0.219
R-Value Observed: 0.221
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.882	α = 90
b = 102.028	β = 90
c = 78.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Baumlova, A.

Boura, E.

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	Project InterBioMed LO1302

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5I0N

PI4K IIalpha bound to calcium

PI4K IIalpha bound to calcium

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)