5EGR

tRNA guanine transglycosylase (TGT) in complex with an Immucillin derivative

• PDB DOI: https://doi.org/10.2210/pdb5EGR/pdb

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


• Deposited: 2015-10-27 Released: 2016-11-09 
• Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Synthesis of an Immucillin Derivative as a Class of tRNA-Guanine Transglycosylase Inhibitors: Exploration of a Transition State Analogous Binding Mode

Ehrmann, F.R., Hohn, C., Haertsch, A., Trapp, N., Heine, A., Klebe, G., Diederich, F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 43.69 kDa 
• Atom Count: 3,112 
• Modelled Residue Count: 362 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NT	G [auth A]	2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one C11 H15 N5 O3 ZIWDWRULEXWPGT-JHYUDYDFSA-N
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.458	α = 90
b = 64.485	β = 93.25
c = 70.978	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2020-08-19
  Changes: Derived calculations
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description