8GEO

E. eligens beta-glucuronidase bound to 3-OH-desloratidine-glucuronide

• PDB DOI: https://doi.org/10.2210/pdb8GEO/pdb

• Classification: HYDROLASE
• Organism(s): Lachnospira eligens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-07 Released: 2024-03-20 
• Deposition Author(s): Simpson, J.B., Redinbo, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.259 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 

Literature

Diverse Human Therapeutics Impact Hormone and Neurotransmitter Homeostasis by Inhibiting Gut Microbial Enzymes

Simpson, J.B., Redinbo, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.52 kDa 
• Atom Count: 4,690 
• Modelled Residue Count: 581 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucuronidase	A	614	Lachnospira eligens	Mutation(s): 0  Gene Names: uidA, ERS852490_00568, ERS852492_02599 EC: 3.2.1.31
UniProt
Find proteins for A0A174ZZA3 (Lachnospira eligens) Explore A0A174ZZA3  Go to UniProtKB:  A0A174ZZA3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZBL (Subject of Investigation/LOI)	B [auth A]	8-chloro-11-(1-beta-D-glucopyranuronosylpiperidin-4-ylidene)-3-hydroxy-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridine C25 H27 Cl N2 O7 ABXRQJRQHLGUBH-OSFFKXSWSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.259 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.066	α = 90
b = 180.066	β = 90
c = 133.826	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Simpson, J.B., Redinbo, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135218

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release