4Q8U | pdb_00004q8u

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

• PDB DOI: https://doi.org/10.2210/pdb4Q8U/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.141 (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: 44.01 kDa 
• Atom Count: 3,293 
• Modeled Residue Count: 369 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2YW	J [auth A]	methyl 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoate C19 H18 N6 O3 OYIIDOTURROWKC-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [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: 1.31 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.751	α = 90
b = 64.49	β = 93.15
c = 70.896	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	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