5YB5

The complex crystal structure of VrEH2 mutant M263N with SNO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation

Li, F.L.Kong, X.D.Chen, Q.Zheng, Y.C.Xu, Q.Chen, F.F.Fan, L.Q.Lin, G.Q.Zhou, J.H.Yu, H.L.Xu, J.H.

(2018) ACS Catal 8: 8314-8317


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epoxide hydrolaseA [auth B]326Vigna radiataMutation(s): 3 
Gene Names: EH2
UniProt
Find proteins for A0A0R5NGA4 (Vigna radiata)
Explore A0A0R5NGA4 
Go to UniProtKB:  A0A0R5NGA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R5NGA4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SNO
Query on SNO

Download Ideal Coordinates CCD File 
B
(S)-PARA-NITROSTYRENE OXIDE
C8 H7 N O3
YKIUTLHCSNCTDZ-MRVPVSSYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.297α = 90
b = 70.297β = 90
c = 121.295γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description