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.
5JSW | pdb_00005jsw
tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3a'R,6'R,6a'R)-2,2,2',2'-tetramethyldihydro-3a'H-spiro[[1,3]dioxolane-4,4'-furo[3,4-d][1,3]dioxol]-6'-yl)methyl)amino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
- PDB DOI: https://doi.org/10.2210/pdb5JSW/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: 1.22 Å
- R-Value Free: 0.144 (Depositor), 0.140 (DCC)
- R-Value Work: 0.125 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.126 (Depositor)
Starting Model: experimental
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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 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 6MM Query on 6MM | N [auth A] | 6-amino-2-({[(3a'R,4S,6'R,6a'R)-2,2,2',2'-tetramethyldihydro-3a'H-spiro[1,3-dioxolane-4,4'-furo[3,4-d][1,3]dioxol]-6'-yl]methyl}amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one (non-preferred name) C21 H26 N6 O6 SAAYEWUENSTOGT-JRMKUOIOSA-N |  | ||
| GOL Query on GOL | G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | C [auth A], D [auth A], E [auth A], F [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | O [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.22 Å
- R-Value Free: 0.144 (Depositor), 0.140 (DCC)
- R-Value Work: 0.125 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.126 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.336 | α = 90 |
| b = 64.956 | β = 96.38 |
| c = 70.782 | 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
