9GMP | pdb_00009gmp

TKUL kinase domain from Leishmania mexicana

• PDB DOI: https://doi.org/10.2210/pdb9GMP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-29 Released: 2025-09-24 
• Deposition Author(s): Fokkens, T.J., Wolter, M., Lorenz, S.
• Funding Organization(s): European Molecular Biology Organization (EMBO), Max Planck Society, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structure of the TKUL kinase domain

Fokkens, T.J., Wolter, M., Lorenz, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.35 kDa 
• Atom Count: 1,972 
• Modeled Residue Count: 241 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein (Map kinase kinase-like protein)	A	285	Leishmania mexicana	Mutation(s): 0  Gene Names: LMXM_34_4000
UniProt
Find proteins for E9B6S8 (Leishmania mexicana (strain MHOM/GT/2001/U1103)) Explore E9B6S8  Go to UniProtKB:  E9B6S8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.092	α = 90
b = 74.565	β = 90
c = 77.734	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Fokkens, T.J., Wolter, M., Lorenz, S.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization (EMBO)	European Union	439-2022
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	GRK2243

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release