5JT6 | pdb_00005jt6

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 2-((2-morpholinoethyl)amino)-1H-benzo[d]imidazole-5-carbohydrazide

• PDB DOI: https://doi.org/10.2210/pdb5JT6/pdb

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


• Deposited: 2016-05-09 Released: 2017-05-24 
• Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines.

Ehrmann, F.R., 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.52 kDa 
• Atom Count: 3,125 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6N1	E [auth A]	2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazole-6-carbohydrazide C14 H20 N6 O2 IGHUHXQGMJQAFS-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.319	α = 90
b = 64.235	β = 92.79
c = 70.985	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: 2017-05-24 
Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description