7EQK

Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions.

Chen, M.H.Li, Y.S.Hsu, N.S.Lin, K.H.Wang, Y.L.Wang, Z.C.Chang, C.F.Lin, J.P.Chang, C.Y.Li, T.L.

(2022) ACS Catal 12: 1945-1956


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin domain-containing protein
A, B
131Streptomyces albusMutation(s): 0 
Gene Names: stnK3G3260_000576
UniProt
Find proteins for L7PIL3 (Streptomyces albus)
Explore L7PIL3 
Go to UniProtKB:  L7PIL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7PIL3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JAX (Subject of Investigation/LOI)
Query on JAX

Download Ideal Coordinates CCD File 
G [auth B](E)-3-(1H-indol-3-yl)-2-oxidanyl-but-2-enoic acid
C12 H11 N O3
PPGRYTGRWGDNAP-YRNVUSSQSA-N
5RN (Subject of Investigation/LOI)
Query on 5RN

Download Ideal Coordinates CCD File 
E [auth A]1-(1~{H}-indol-3-yl)ethanone
C10 H9 N O
VUIMBZIZZFSQEE-UHFFFAOYSA-N
GOA (Subject of Investigation/LOI)
Query on GOA

Download Ideal Coordinates CCD File 
D [auth A]GLYCOLIC ACID
C2 H4 O3
AEMRFAOFKBGASW-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.782α = 90
b = 66.782β = 90
c = 116.336γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2023-11-29
    Changes: Refinement description