5FEA | pdb_00005fea

Domain Swapped Bromodomain from Leishmania donovani

• PDB DOI: https://doi.org/10.2210/pdb5FEA/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Leishmania donovani BPK282A1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-16 Released: 2016-01-13 
• Deposition Author(s): Walker, J.R., Hou, C.F.D., Lin, Y.H., LOPPNAU, P., Dong, A., El Bakkouri, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.277 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Domain Swapped Bromodomain from Leishmania donovani

Walker, J.R., Hou, C.F.D., Lin, Y.H., LOPPNAU, P., Dong, A., El Bakkouri, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Structural Genomics Consortium (SGC)

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)

Macromolecule Content 

• Total Structure Weight: 32.37 kDa 
• Atom Count: 2,011 
• Modeled Residue Count: 246 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	136	Leishmania donovani BPK282A1	Mutation(s): 0  Gene Names: LDBPK_363520
UniProt
Find proteins for A0A3S7XB61 (Leishmania donovani) Explore A0A3S7XB61  Go to UniProtKB:  A0A3S7XB61

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMF	D [auth B], E [auth B]	Bromosporine C17 H20 N6 O4 S UYBRROMMFMPJAN-UHFFFAOYSA-N
BR	C [auth A], F [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.277 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.176	α = 90
b = 77.176	β = 90
c = 169.496	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Walker, J.R., Hou, C.F.D., Lin, Y.H., LOPPNAU, P., Dong, A., El Bakkouri, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description