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

PDB DOI: https://doi.org/10.2210/pdb5LPP/pdb

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

Deposited: 2016-08-14 Released: 2017-08-30
Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

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.

Macromolecule Content

Total Structure Weight: 43.42 kDa
Atom Count: 2,782
Modelled Residue Count: 340
Deposited Residue Count: 386
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	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
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
72C Query on 72C 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]	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		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] 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: 1.99 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 = 85.423	α = 90
b = 64.443	β = 93.88
c = 71.223	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

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

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.