6YGS | pdb_00006ygs

tRNA-guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-(methylamino)-4-(4-(trifluoromethyl)phenethyl)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

PDB DOI: https://doi.org/10.2210/pdb6YGS/pdb

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

Deposited: 2020-03-27 Released: 2020-04-08
Deposition Author(s): Nguyen, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.164 (Depositor), 0.165 (DCC)
R-Value Work:
0.135 (Depositor), 0.138 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 43.63 kDa
Atom Count: 3,152
Modeled Residue Count: 351
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	388	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OQQ Query on OQQ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	6-amino-2-(methylamino)-4-(4-(trifluoromethyl)phenethyl)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one C₁₉ H₁₇ F₃ N₆ O ZWUPQNLDYYEWTK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.164 (Depositor), 0.165 (DCC)
R-Value Work: 0.135 (Depositor), 0.138 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.974	α = 90
b = 64.822	β = 93.866
c = 71.464	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

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, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.