6CHK

Crystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound TRIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Automatic recognition of ligands in electron density by machine learning.

Kowiel, M.Brzezinski, D.Porebski, P.J.Shabalin, I.G.Jaskolski, M.Minor, W.

(2019) Bioinformatics 35: 452-461

  • DOI: https://doi.org/10.1093/bioinformatics/bty626
  • Primary Citation of Related Structures:  
    6CHK

  • PubMed Abstract: 

    The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting. Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identification, in some cases doubling the recognition rates, while requiring significantly less time. Our work shows that machine learning can improve the automation of structure modeling and significantly accelerate the drug screening process of macromolecule-ligand complexes. Code and data are available on GitHub at https://github.com/dabrze/CheckMyBlob. Supplementary data are available at Bioinformatics online.


  • Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, LacI family282Lacticaseibacillus paracasei ATCC 334Mutation(s): 0 
Gene Names: LSEI_2103
UniProt
Find proteins for Q036L9 (Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 / NRRL B-441))
Explore Q036L9 
Go to UniProtKB:  Q036L9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ036L9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.715α = 90
b = 108.715β = 90
c = 125.395γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXphasing
SHELXmodel building
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesHG008424
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117325
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117080

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence, Database references
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Derived calculations