5I00 | pdb_00005i00

tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclopentylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

PDB DOI: https://doi.org/10.2210/pdb5I00/pdb

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

Deposited: 2016-02-03 Released: 2017-02-15
Deposition Author(s): Ehrmann, F.R., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.156 (Depositor), 0.157 (DCC)
R-Value Work:
0.125 (Depositor), 0.126 (DCC)
R-Value Observed:
0.126 (Depositor)

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

Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors

Ehrmann, F.R., Stojko, J., Reuter, K., Heine, A., Klebe, G., Sanglier-Cianferani, S., Diederich, F.

To be published.

Macromolecule Content

Total Structure Weight: 43.73 kDa
Atom Count: 3,473
Modeled Residue Count: 370
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	385	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AFQ Query on AFQ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	6-amino-4-{2-[(cyclopentylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one C₁₈ H₂₅ N₇ O OTRZFAIJJHPZSL-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [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]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.156 (Depositor), 0.157 (DCC)
R-Value Work: 0.125 (Depositor), 0.126 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.299	α = 90
b = 65.114	β = 96.25
c = 70.644	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

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Entry History

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Ehrmann, F.R.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2017-02-15
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description

5I00 | pdb_00005i00

tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclopentylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Literature

Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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