5LPP

tRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group C2) with 6-amino-4-(2-((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)ethyl)-2-(methylamino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Carbohydrate-based Inhibitors targeting the Ribose-34 pocket of Z.mobilis TGT and changing the oligomeric state of the homodimer

Ehrmann, F.R.Botzanowski, T.Pfaffender, T.Heine, A.Diederich, F.Sanglier-Cianferani, S.Klebe, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Queuine tRNA-ribosyltransferase386Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821Mutation(s): 0 
Gene Names: tgtZMO0363
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
72C
Query on 72C

Download Ideal Coordinates CCD File 
C [auth A]4-[2-[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-methoxy-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]ethyl]-6-azanyl-2-(methylamino)-1,7-dihydroimidazo[4,5-g]quinazolin-8-one
C20 H26 N6 O5
VLKGVMAOHRTCMF-BNGXUDDSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.423α = 90
b = 64.443β = 93.88
c = 71.223γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description