Download MendeleyApplication of carbohydrates based lin-benzoguanines in a solvent-exposed subpocket of the tRNA-modifying Enzyme TGT
Ehrmann, F.R., Schaefer, E., Heine, A., Diederich, F., Klebe, G.To be published.
5JSV
tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)methyl)amino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
- PDB DOI: https://doi.org/10.2210/pdb5JSV/pdb
- Classification: TRANSFERASE
- Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-05-09 Released: 2017-05-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.17 Å
- R-Value Free: 0.139
- R-Value Work: 0.121
- R-Value Observed: 0.122
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Queuine tRNA-ribosyltransferase | 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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 6MQ Query on 6MQ | G [auth A] | methyl 5-[(6-amino-8-oxo-7,8-dihydro-3H-imidazo[4,5-g]quinazolin-2-yl)amino]-5-deoxy-2,3-O-(1-methylethylidene)-beta-D-ribofuranoside C18 H22 N6 O5 DVNDKLBXQGGFSV-RGCMKSIDSA-N |  | ||
| GOL Query on GOL | C [auth A], D [auth A], E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.17 Å
- R-Value Free: 0.139
- R-Value Work: 0.121
- R-Value Observed: 0.122
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.505 | α = 90 |
| b = 65.2 | β = 96.44 |
| c = 70.598 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2017-05-24 Deposition Author(s): Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2017-05-24
Type: Initial release - Version 1.1: 2018-03-07
Changes: Data collection - Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
