4ETJ

Crystal Structure of E6H variant of de novo designed serine hydrolase OSH55, Northeast Structural Genomics Consortium (NESG) Target OR185


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design of activated serine-containing catalytic triads with atomic-level accuracy.

Rajagopalan, S.Wang, C.Yu, K.Kuzin, A.P.Richter, F.Lew, S.Miklos, A.E.Matthews, M.L.Seetharaman, J.Su, M.Hunt, J.F.Cravatt, B.F.Baker, D.

(2014) Nat Chem Biol 10: 386-391

  • DOI: https://doi.org/10.1038/nchembio.1498
  • Primary Citation of Related Structures:  
    3TP4, 3V45, 4DRT, 4ESS, 4ETJ, 4ETK, 4F2V, 4JCA, 4JLL, 4JVV

  • PubMed Abstract: 

    A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.


  • Organizational Affiliation

    1] Department of Biochemistry, University of Washington, Seattle, Washington, United States. [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydrolase167synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE5
Query on PE5

Download Ideal Coordinates CCD File 
D [auth A]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
PE6
Query on PE6

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHORYL-HEXAETHYLENE GLYCOL
C12 H27 O10 P
PTMCGHPIYOSATH-UHFFFAOYSA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
C [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.93α = 90
b = 65.93β = 90
c = 89.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-05-14
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary