9LZI | pdb_00009lzi

Crystal structure of glycerol kinase from Entamoeba histolytica complexed with GK-butyl.

PDB DOI: https://doi.org/10.2210/pdb9LZI/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: 1.89 Å
R-Value Free:
0.225 (Depositor), 0.229 (DCC)
R-Value Work:
0.193 (Depositor), 0.202 (DCC)
R-Value Observed:
0.195 (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: 108.72 kDa
Atom Count: 7,762
Modeled Residue Count: 971
Deposited Residue Count: 972
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	486	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6Y0 (Subject of Investigation/LOI) Query on 6Y0 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	4-butyl-7,8-bis(oxidanyl)chromen-2-one C₁₃ H₁₄ O₄ GDGBIWNBPUQGGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A], E [auth A], K [auth B], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]