5TCM | pdb_00005tcm

First Bromodomain from Leishmania donovani LdBPK.091320 complexed with BI-2536

• PDB DOI: https://doi.org/10.2210/pdb5TCM/pdb

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


• Deposited: 2016-09-15 Released: 2016-10-05 
• Deposition Author(s): Lin, Y.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: 2.20 Å
• R-Value Free: 
  0.218 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

First Bromodomain from Leishmania donovani LdBPK.091320 complexed with BI-2536

Lin, Y.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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.72 kDa 
• Atom Count: 3,040 
• Modeled Residue Count: 346 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	130	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R78	D [auth A], F [auth B], I [auth C]	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide C28 H39 N7 O3 XQVVPGYIWAGRNI-JOCHJYFZSA-N
EDO	E [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.218 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.332	α = 90
b = 85.25	β = 94.46
c = 57.277	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Lin, Y.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: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2018-04-18
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary