8Y1T | pdb_00008y1t

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE COMPLEX WITH ADP and G3P

PDB DOI: https://doi.org/10.2210/pdb8Y1T/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma brucei gambiense
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-25 Released: 2025-01-29
Deposition Author(s): Balogun, E.O., Inaoka, D.K., Ichinose, M., Chishima, T., Harada, S., Kita, K., Shiba, T.
Funding Organization(s): National Institutes of Health/John E. Fogarty International Center (NIH/FIC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.250 (Depositor), 0.257 (DCC)
R-Value Work:
0.192 (Depositor), 0.207 (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

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE COMPLEX WITH ADP and G3P

Balogun, E.O., Inaoka, D.K., Ichinose, M., Chishima, T., Harada, S., Kita, K., Shiba, T.

To be published.

Macromolecule Content

Total Structure Weight: 115.36 kDa
Atom Count: 7,989
Modeled Residue Count: 1,028
Deposited Residue Count: 1,036
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	518	Trypanosoma brucei gambiense	Mutation(s): 0 Gene Names: gk EC: 2.7.1.30
UniProt
Find proteins for Q9NJP9 (Trypanosoma brucei brucei) Explore Q9NJP9 Go to UniProtKB: Q9NJP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NJP9
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 D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
G3P (Subject of Investigation/LOI) Query on G3P Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	F [auth B], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]