2QZR

tRNA-Guanine Transglycosylase(TGT) in Complex with 6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

PDB DOI: https://doi.org/10.2210/pdb2QZR/pdb

Classification: TRANSFERASE
Organism(s): Zymomonas mobilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-17 Released: 2007-09-11
Deposition Author(s): Hoertner, S.R., Ritschel, T., Stengl, B., Kramer, C., Schweizer, W.B., Wagner, B., Kansy, M., Klebe, G., Diederich, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.259
R-Value Work: 0.198
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Potent Inhibitors of tRNA-Guanine Transglycosylase, an Enzyme Linked to the Pathogenicity of the Shigella Bacterium: Charge-Assisted Hydrogen Bonding.

Hortner, S.R., Ritschel, T., Stengl, B., Kramer, C., Schweizer, W.B., Wagner, B., Kansy, M., Klebe, G., Diederich, F.

(2007) Angew Chem Int Ed Engl 46: 8266-8269

PubMed: 17902085 Search on PubMed
DOI: https://doi.org/10.1002/anie.200702961
Primary Citation of Related Structures:
2QZR

Organizational Affiliation

Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 43.4 kDa
Atom Count: 3,023
Modelled Residue Count: 359
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	385	Zymomonas mobilis	Mutation(s): 0 Gene Names: tgt 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S79 Query on S79 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one C₂₀ H₁₆ N₆ O MCEZMMDIEXECTI-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] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [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]

Binding Affinity Annotations
ID	Source	Binding Affinity
S79	PDBBind: 2QZR	Ki: 55 (nM) from 1 assay(s)
S79	Binding MOAD: 2QZR	Ki: 55 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.259
R-Value Work: 0.198
R-Value Observed: 0.198
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.085	α = 90
b = 63.44	β = 93.3
c = 71.123	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-08-19
Changes: Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description

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Help and Resources

2QZR

tRNA-Guanine Transglycosylase(TGT) in Complex with 6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Potent Inhibitors of tRNA-Guanine Transglycosylase, an Enzyme Linked to the Pathogenicity of the Shigella Bacterium: Charge-Assisted Hydrogen Bonding.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)