9LYY | pdb_00009lyy

Crystal structure of glycerol kinase from Entamoeba histolytica complexed with ADP and G3P.

PDB DOI: https://doi.org/10.2210/pdb9LYY/pdb

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

Deposited: 2025-02-21 Released: 2026-02-25
Deposition Author(s): Balogun, E.O., Jeelani, G., Hane, E., Kondo, H., Hasegawa, Y., Kojima, C., Chishima, T., Harada, S., Kishikawa, J., Nozaki, T., Shiba, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.206 (Depositor), 0.213 (DCC)
R-Value Work:
0.186 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insights into the reverse reaction mechanism of glycerol kinase from Entamoeba histolytica

Balogun, E.O., Jeelani, G., Hane, E., Kondo, H., Hasegawa, Y., Kojima, C., Chishima, T., Harada, S., Kishikawa, J., Nozaki, T., Shiba, T.

To be published.

Macromolecule Content

Total Structure Weight: 109.22 kDa
Atom Count: 7,967
Modeled Residue Count: 972
Deposited Residue Count: 974
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B	487	Entamoeba histolytica	Mutation(s): 0 Gene Names: CL6EHI_164850 EC: 2.7.1.30
UniProt
Find proteins for A0A5K1V6Z1 (Entamoeba histolytica) Explore A0A5K1V6Z1 Go to UniProtKB: A0A5K1V6Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5K1V6Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
G3P (Subject of Investigation/LOI) Query on G3P Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]