6YYZ

tRNA-Guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

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

Co-crystallization, 19F NMR and nanoESI-MS reveal dimer disturbing inhibitors and conformational changes at dimer contacts

Nguyen, A.Heine, A.Klebe, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Queuine tRNA-ribosyltransferase388Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821Mutation(s): 1 
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
725 (Subject of Investigation/LOI)
Query on 725

Download Ideal Coordinates CCD File 
C [auth A]6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
C19 H26 N6 O5
OMBPYCFBGGXDQG-BNGXUDDSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FTR
Query on FTR
A
L-PEPTIDE LINKINGC11 H11 F N2 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.723α = 90
b = 65.036β = 93.712
c = 71.568γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description