4FPS | pdb_00004fps

tRNA-Guanine Transglycosylase in complex with adamantyl-substituted lin-benzoguanine ligand

• PDB DOI: https://doi.org/10.2210/pdb4FPS/pdb

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


• Deposited: 2012-06-22 Released: 2013-07-24 
• Deposition Author(s): Immekus, F., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.197 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Studies on TGT homodimer interface

Immekus, F., Barandun, L.J., Betz, M., Debaene, F., Petiot, S., Sanglier-Cianferani, S., 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: 43.5 kDa 
• Atom Count: 3,032 
• Modeled Residue Count: 363 
• 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
0UX	C [auth A]	6-amino-2-(methylamino)-4-(2-{[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-ylmethyl]amino}ethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one C23 H31 N7 O HJDZMDZEUQKVPL-CAUGRDAOSA-N
GOL	D [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: 1.45 Å
• R-Value Free:  0.197 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.01	α = 90
b = 64.72	β = 96.02
c = 70.7	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Immekus, F., Klebe, G.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description