4Q8V

tRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amino-8-oxo-1H,7H,8H-imidazo[4,5-g]quinazolin-2-yl}amino)ethyl]benzonitrile

• PDB DOI: https://doi.org/10.2210/pdb4Q8V/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-28 Released: 2015-05-20 
• Deposition Author(s): Neeb, M., Heine, A., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Addressing a New Subpocket of TGT by Elongated 2-Amino-lin-benzoguanines

Neeb, M., Hohn, C., Heine, A., Diederich, F., Klebe, G.

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: 43.57 kDa 
• Atom Count: 3,331 
• Modelled Residue Count: 370 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	388	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2YX	D [auth A]	4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzonitrile C18 H15 N7 O NYFZULJQMISTPE-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.164	α = 90
b = 65.098	β = 96.31
c = 70.76	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Neeb, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description