6PDH

Crystal Structure of EcDsbA in a complex with purified pyrazole 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

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

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein DsbA
A, B
189Escherichia coli K-12Mutation(s): 0 
Gene Names: dsbAdsfppfAb3860JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Explore P0AEG4 
Go to UniProtKB:  P0AEG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEG4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OAV (Subject of Investigation/LOI)
Query on OAV

Download Ideal Coordinates CCD File 
C [auth A]2-[4-(4-cyano-3-methylphenoxy)phenyl]-N-ethyl-N-[2-(1H-pyrazol-1-yl)ethyl]acetamide
C23 H24 N4 O2
ABKHTUJKHPJZLS-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OAV Binding MOAD:  6PDH Kd: 6.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.214α = 90
b = 50.295β = 118.113
c = 91.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaProject Grant APP1099151
Australian Research Council (ARC)AustraliaLIEF LE160100047

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description