5TCK | pdb_00005tck

Second Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine

• PDB DOI: https://doi.org/10.2210/pdb5TCK/pdb

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


• Deposited: 2016-09-15 Released: 2016-11-09 
• Deposition Author(s): Lin, L.-H., Hou, C.F.D., Loppnau, P., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.238 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Second Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine

Lin, L.-H., Hou, C.F.D., Loppnau, P., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 37.1 kDa 
• Atom Count: 2,466 
• Modeled Residue Count: 276 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	157	Leishmania donovani BPK282A1	Mutation(s): 0  Gene Names: LDBPK_091320
UniProt
Find proteins for A0A3Q8I8I6 (Leishmania donovani) Explore A0A3Q8I8I6  Go to UniProtKB:  A0A3Q8I8I6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMF	C [auth A], G [auth B]	Bromosporine C17 H20 N6 O4 S UYBRROMMFMPJAN-UHFFFAOYSA-N
BME	D [auth A], H [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	F [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SX	E [auth A], I [auth B]	SULFUR OXIDE O S XTQHKBHJIVJGKJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.238 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.245	α = 90
b = 74.086	β = 90
c = 106.412	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
Arcimboldo	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Lin, L.-H., Hou, C.F.D., Loppnau, P., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Structure summary