1K4H

CRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COMPLEXED WITH 2,6-Diamino-8-propylsulfanylmethyl-3H-quinazoline-4-one

• PDB DOI: https://doi.org/10.2210/pdb1K4H/pdb

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


• Deposited: 2001-10-08 Released: 2002-04-24 
• Deposition Author(s): Brenk, R., Meyer, E.A., Castellano, R.K., Furler, M., Stubbs, M.T., Klebe, G., Diederich, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 

Literature

De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity.

Meyer, E.A., Brenk, R., Castellano, R.K., Furler, M., Klebe, G., Diederich, F.

(2002) Chembiochem 3: 250-253

• PubMed: 11921407 
• DOI: https://doi.org/10.1002/1439-7633(20020301)3:2/3<250::AID-CBIC250>3.0.CO;2-J
• Primary Citation of Related Structures:  
  1K4G, 1K4H

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Organizational Affiliation: 

Laboratorium für Organische Chemie, ETH-Hönggerberg, HCI, 8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.26 kDa 
• Atom Count: 3,327 
• Modelled Residue Count: 372 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNA-GUANINE-TRANSGLYCOSYLASE	A	386	Zymomonas mobilis	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APQ	C [auth A]	2,6-DIAMINO-8-PROPYLSULFANYLMETHYL-3H-QUINAZOLINE-4-ONE C12 H16 N4 O S RSKNEWMEOVQZII-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
APQ	Binding MOAD:  1K4H	Ki: 7700 (nM) from 1 assay(s)
	PDBBind:  1K4H	Ki: 7700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.71	α = 90
b = 64.99	β = 96.44
c = 71.07	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-24 
Deposition Author(s): Brenk, R., Meyer, E.A., Castellano, R.K., Furler, M., Stubbs, M.T., Klebe, G., Diederich, F.

Revision History  

• Version 1.0: 2002-04-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-08-19
  Changes: Advisory, Derived calculations
• Version 1.4: 2023-08-16
  Changes: Advisory, Data collection, Database references, Refinement description