23VK | pdb_000023vk

Crystal structure of full-length of APS kinase from Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb23VK/pdb

Classification: TRANSFERASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-20 Released: 2026-06-03
Deposition Author(s): Hatanaka, R., Yuasa, H., Inoguchi, A., Matsui, H., Osumi, Y., Mi-ichi, F., Kishikawa, J., Shiba, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.265 (Depositor), 0.266 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 23VK

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into interdomain interactions in Entamoeba histolytica APS kinase.

Hatanaka, R., Osumi, Y., Matsui, H., Inoguchi, A., Yuasa, H., Mi-ichi, F., Kishikawa, J., Shiba, T.

(2026) J Struct Biol X 13

DOI: https://doi.org/10.1016/j.yjsbx.2026.100147

Macromolecule Content

Total Structure Weight: 222.84 kDa
Atom Count: 14,098
Modeled Residue Count: 1,806
Deposited Residue Count: 2,000
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adenylyl-sulfate kinase	A, B, C, D	500	Entamoeba histolytica	Mutation(s): 0 Gene Names: CL6EHI_179080 EC: 2.7.1.25
UniProt
Find proteins for A0A5K1U9J0 (Entamoeba histolytica) Explore A0A5K1U9J0 Go to UniProtKB: A0A5K1U9J0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5K1U9J0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265 (Depositor), 0.266 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.449	α = 90
b = 158.387	β = 90
c = 226.163	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CRANK2	phasing
BUCCANEER	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	Grant-in-Aid for Scientific Research(B), 25K02488

Revision History (Full details and data files)

Version 1.0: 2026-06-03
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.