6BYA | pdb_00006bya

Crystal structure of LdBPK_091320 with inhibitor bound

• PDB DOI: https://doi.org/10.2210/pdb6BYA/pdb

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


• Deposited: 2017-12-20 Released: 2018-01-17 
• Deposition Author(s): Dong, A., Lin, Y.H., Loppnau, P., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.239 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of LdBPK_091320.1 with with inhibitor bound

Lin, Y.H., Dong, A., Loppnau, P., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, 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)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.53 kDa 
• Atom Count: 3,822 
• Modeled Residue Count: 472 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	133	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
2LO	E [auth A], G [auth B], I [auth C], K [auth D]	2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole C28 H33 Cl N4 O3 GEPYBHCJBORHCE-SFHVURJKSA-N
UNX	F [auth A], H [auth B], J [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.239 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36BYA

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.615	α = 90
b = 82.615	β = 90
c = 177.235	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Dong, A., Lin, Y.H., Loppnau, P., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description