RCSB PDB - 8AGS: Cyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site

 8AGS

Cyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2CHClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Complexes of epoxide hydrolase from metagenomic source ch65

Isupov, M.N.De Rose, S.A.Mitchell, D.Littlechild, J.A.Parker, E.Ferrandi, E.Guazzelli, E.Monti, D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha/beta epoxide hydrolaseA [auth AAA],
B [auth BBB]
299metagenomeMutation(s): 0 
UniProt
Find proteins for A0A1U9WZ52 (uncultured bacterium)
Explore A0A1U9WZ52 
Go to UniProtKB:  A0A1U9WZ52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U9WZ52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
M [auth BBB]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth AAA]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
2CH (Subject of Investigation/LOI)
Query on 2CH

Download Ideal Coordinates CCD File 
C [auth AAA],
N [auth BBB]
2-CHLOROPHENOL
C6 H5 Cl O
ISPYQTSUDJAMAB-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth AAA]
F [auth AAA]
G [auth AAA]
H [auth AAA]
I [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth AAA],
L [auth AAA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.21α = 90
b = 46.19β = 98
c = 92.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
BUSTERrefinement
PARROTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2CHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union265933

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release