5C4Q | pdb_00005c4q

Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine

• PDB DOI: https://doi.org/10.2210/pdb5C4Q/pdb

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


• Deposited: 2015-06-18 Released: 2015-07-08 
• Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Hou, C.F.D., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine

Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Hou, C.F.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry, gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: mass spectrometry, gel filtration

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.69 kDa 
• Atom Count: 2,071 
• Modeled Residue Count: 232 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain	A, B	125	Leishmania donovani BPK282A1	Mutation(s): 0  Gene Names: LDBPK_363130
UniProt
Find proteins for A0A3Q8IW45 (Leishmania donovani) Explore A0A3Q8IW45  Go to UniProtKB:  A0A3Q8IW45

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMF	C [auth A], H [auth B]	Bromosporine C17 H20 N6 O4 S UYBRROMMFMPJAN-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.916	α = 90
b = 34.385	β = 117.58
c = 86.463	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Hou, C.F.D., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description