7S1D

Crystal structure of E.coli DsbA in complex with compound MIPS-0001877 (compound 39)

• PDB DOI: https://doi.org/10.2210/pdb7S1D/pdb

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


• Deposited: 2021-09-02 Released: 2023-02-08 
• Deposition Author(s): Heras, B., Scanlon, M.J., Martin, J.L., Caria, S.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.194 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Fluoromethylketone-fragment conjugates designed as covalent modifiers of EcDsbA are atypical substrates

Bradley, C.D., Whitehouse, R.L., Rimmer, K., Williams, M., Heras, B., Caria, S., Ilyichova, O., Vazirani, M., Mohanty, B., Harper, J., Scanlon, M.J., Simpson, J.S.

(2022) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2022-262lh

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.71 kDa 
• Atom Count: 3,504 
• Modelled 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 DsbA	A, B	189	Escherichia coli K-12	Mutation(s): 0  Gene Names: dsbA, dsf, ppfA, b3860, JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
648 (Subject of Investigation/LOI)	C [auth A]	1-[3-(thiophen-3-yl)benzyl]piperidin-2-one C16 H17 N O S UMRKGGGHCYSVML-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	D [auth B], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.194 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.966	α = 90
b = 64.22	β = 126.04
c = 74.356	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Heras, B., Scanlon, M.J., Martin, J.L., Caria, S.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT455860

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description