1K4H | pdb_00001k4h

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.229 (Depositor), 0.220 (DCC)
R-Value Work:
0.196 (Depositor), 0.191 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APQ Query on APQ 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]	2,6-DIAMINO-8-PROPYLSULFANYLMETHYL-3H-QUINAZOLINE-4-ONE C₁₂ H₁₆ N₄ O S RSKNEWMEOVQZII-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] 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: 1.80 Å
R-Value Free: 0.229 (Depositor), 0.220 (DCC)
R-Value Work: 0.196 (Depositor), 0.191 (DCC)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-04-24

Deposition Author(s):

Revision History (Full details and data files)

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