Download MendeleyCo-crystallization, nanoESI-MS and 19F NMR reveal dimer disturbing inhibitors and conformational changes at dimer contacts
Nguyen, A., Heine, A., Klebe, G.To be published.
6YHD | pdb_00006yhd
tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-4-(2-((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)ethyl)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
- PDB DOI: https://doi.org/10.2210/pdb6YHD/pdb
- Classification: TRANSFERASE
- Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2020-03-28 Released: 2020-04-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.144 (Depositor), 0.140 (DCC)
- R-Value Work: 0.121 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.122 (Depositor)
Starting Model: experimental
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This is version 1.1 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 | 388 | Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 | Mutation(s): 1 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 | |
| 1WK (Subject of Investigation/LOI) Query on 1WK | B [auth A] | methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-beta-D-ribo-hexofuranoside C17 H22 N6 O5 VKQAJTKFJIETGO-QGMIFYJMSA-N |  | ||
| GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | F [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| FTR Query on FTR | A | L-PEPTIDE LINKING | C11 H11 F N2 O2 |  | TRP |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.144 (Depositor), 0.140 (DCC)
- R-Value Work: 0.121 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.122 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.579 | α = 90 |
| b = 65.369 | β = 96.129 |
| c = 70.564 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Coot | model building |
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2020-04-08 Deposition Author(s): Nguyen, A., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2020-04-08
Type: Initial release - Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
