9GJR | pdb_00009gjr

Crystal Structure of the Leishmania Bromodomain LmxBDF5.1 in complex with OXFBD06

• PDB DOI: https://doi.org/10.2210/pdb9GJR/pdb

• Classification: TRANSCRIPTION
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-08-22 Released: 2025-09-03 
• Deposition Author(s): Amann, M., Huegle, M., Carter, J., Einsle, O., Guenther, S., Conway, S.
• Funding Organization(s): Other government, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.170 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of the Leishmania Bromodomain LmxBDF5.1 in complex with OXFBD06

Amann, M., Huegle, M., Carter, J., Einsle, O., Guenther, S., Conway, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.35 kDa 
• Atom Count: 2,300 
• Modeled Residue Count: 228 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromo domain-containing protein	A, B [auth C]	114	Leishmania mexicana	Mutation(s): 0  Gene Names: LMXM_09_1260
UniProt
Find proteins for E9AMX7 (Leishmania mexicana (strain MHOM/GT/2001/U1103)) Explore E9AMX7  Go to UniProtKB:  E9AMX7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IMI (Subject of Investigation/LOI)	C [auth A], D [auth C]	5-[2-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(4-ethanoylpiperazin-1-ium-1-yl)ethyl]benzimidazol-2-yl]ethyl]-2-methyl-benzenecarbonitrile C30 H35 N6 O2 MBOHTEXMGONSHT-UHFFFAOYSA-O
BU3	E [auth C]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N
K	F [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.170 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.794	α = 90
b = 49.646	β = 90
c = 85.634	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Amann, M., Huegle, M., Carter, J., Einsle, O., Guenther, S., Conway, S.

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Funding Organization	Location	Grant Number
Other government		EP/R513295/1
German Research Foundation (DFG)	Germany	RTG2202

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release