6J9Q | pdb_00006j9q

Crystal structure of Trypanosoma brucei gambiense glycerol kinase complex with AMP-PNP.

• PDB DOI: https://doi.org/10.2210/pdb6J9Q/pdb

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


• Deposited: 2019-01-24 Released: 2020-01-29 
• Deposition Author(s): Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Reaction mechanism of the reverse reaction of African human trypanosomes glycerol kinase.

Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 230.84 kDa 
• Atom Count: 16,007 
• Modeled Residue Count: 2,052 
• Deposited Residue Count: 2,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	A, B, C, D	518	Trypanosoma brucei gambiense	Mutation(s): 0  Gene Names: gk EC: 2.7.1.30
UniProt
Find proteins for D3KVM3 (Trypanosoma brucei gambiense) Explore D3KVM3  Go to UniProtKB:  D3KVM3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	F [auth A], I [auth B], K [auth C], M [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	E [auth A], G [auth B], H [auth B], J [auth C], L [auth D], N [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.598	α = 90
b = 123.149	β = 90
c = 154.223	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary