6YGZ

tRNA Guanine Transglycosylase (TGT) labelled with 5-fluoro-tryptophan in co-crystallized complex with 6-Amino-4-(2-phenylethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

PDB DOI: https://doi.org/10.2210/pdb6YGZ/pdb

Classification: TRANSFERASE
Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-03-28 Released: 2020-04-08
Deposition Author(s): Nguyen, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.248
R-Value Work: 0.213
R-Value Observed: 0.215

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.

Macromolecule Content

Total Structure Weight: 43.51 kDa
Atom Count: 2,872
Modelled Residue Count: 352
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	388	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NE8 (Subject of Investigation/LOI) Query on NE8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE C₁₇ H₁₅ N₅ O PBZAIUVFRISTSZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FTR Query on FTR	A	L-PEPTIDE LINKING	C₁₁ H₁₁ F N₂ O₂		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.248
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.8	α = 90
b = 64.904	β = 94.135
c = 71.299	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Nguyen, A.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

6YGZ

tRNA Guanine Transglycosylase (TGT) labelled with 5-fluoro-tryptophan in co-crystallized complex with 6-Amino-4-(2-phenylethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)