23VL | pdb_000023vl

Crystal structure of AS-like domain of APS kinase from Entamoeba histolytica

• PDB DOI: https://doi.org/10.2210/pdb23VL/pdb

• Classification: SULFATE ACTIVATION
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.36 kDa 
• Atom Count: 2,284 
• Modeled Residue Count: 289 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adenylyl-sulfate kinase	A	317	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.634	α = 90
b = 55.695	β = 90
c = 105.765	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Hatanaka, R., Yuasa, H., Inoguchi, A., Matsui, H., Osumi, Y., Mi-ichi, F., Kishikawa, J., Shiba, T.

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

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release