5QKU | pdb_00005qku

Group deposition of library data - Crystal Structure of EcDsbA after initial refinement with no ligand modelled (structure B1_1)

• PDB DOI: https://doi.org/10.2210/pdb5QKU/pdb
• Deposition Group: G_1002060 | Explore  G_1002060  

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-27 Released: 2020-02-05 
• Deposition Author(s): Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.302 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX).

Bentley, M.R., Ilyichova, O.V., Wang, G., Williams, M.L., Sharma, G., Alwan, W.S., Whitehouse, R.L., Mohanty, B., Scammells, P.J., Heras, B., Martin, J.L., Totsika, M., Capuano, B., Doak, B.C., Scanlon, M.J.

(2020) J Med Chem 63: 6863-6875

• PubMed: 32529824 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00111
• Primary Citation Related Structures: 
  5QKC, 5QKD, 5QKE, 5QKF, 5QKG, 5QKH, 5QKI, 5QKJ, 5QKK, 5QKL, 5QKM, 5QKN, 5QKO, 5QKP, 5QKQ, 5QKR, 5QKS, 5QKT, 5QKU, 5QKV, 5QKW, 5QKX, 5QKY, 5QKZ, 5QL0, 5QL1, 5QL2, 5QL3, 5QL4, 5QL5, 5QL6, 5QL7, 5QL8, 5QL9, 5QLA, 5QLB, 5QLC, 5QLD, 5QLE, 5QLF, 5QLG, 5QLH, 5QLI, 5QLJ, 5QLK, 5QLL, 5QLM, 5QLN, 5QLO, 5QLP, ... Search all related entries


• PubMed Abstract: 
  

  A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein, we describe an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis. This approach yielded an 8-fold increase in affinity and detailed structural information for the resulting complex, providing an efficient and broadly applicable approach to early fragment development.

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Organizational Affiliation: 
• Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
Griffith Institute for Drug Discovery, Building N75, Brisbane Innovation Park, Don Young Road, Nathan, QLD 4111, Australia.
Vice-Chancellor's Unit, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.
Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.31 kDa 
• Atom Count: 3,064 
• Modeled Residue Count: 376 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein	A, B	189	Escherichia coli K-12	Mutation(s): 0  Gene Names: dsbA
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.302 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.827	α = 90
b = 64.717	β = 125.76
c = 74.422	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J.

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2020-07-22
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary