5LPQ

tRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group P21) with 6-amino-4-(2-((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)ethyl)-2-(methylamino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one

• PDB DOI: https://doi.org/10.2210/pdb5LPQ/pdb

• Classification: TRANSFERASE
• Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-14 Released: 2017-08-30 
• Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.262 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Starting Model: experimental

Literature

Carbohydrate-based Inhibitors targeting the Ribose-34 pocket of Z.mobilis TGT and changing the oligomeric state of the homodimer

Ehrmann, F.R., Botzanowski, T., Pfaffender, T., Heine, A., Diederich, F., Sanglier-Cianferani, S., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.84 kDa 
• Atom Count: 5,610 
• Modelled Residue Count: 729 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A, B	386	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 0  Gene Names: tgt, ZMO0363 EC: 2.4.2.29
UniProt
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore P28720  Go to UniProtKB:  P28720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
72C	D [auth A], F [auth B]	4-[2-[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-methoxy-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]ethyl]-6-azanyl-2-(methylamino)-1,7-dihydroimidazo[4,5-g]quinazolin-8-one C20 H26 N6 O5 VLKGVMAOHRTCMF-BNGXUDDSSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.262 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.9	α = 90
b = 78.851	β = 109.72
c = 84.943	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description