Research workbench
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
Analyse TRNA-guanine transglycosylase (tgt) labeled with 5-fluorotryptophan in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YHD
- Type
- protein
- Length
- 371 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Queuine tRNA-ribosyltransferase
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- 1WK, ZN, CL
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 371 | 47% helix, 19% strand | P28720 |
Ligands and binding sites
- 1WK · 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 · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.56 | 0.81 | 28 | 1WK |
| 2 | 61 | 0.31 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6YHD · tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P28720
- Elsewhere: RCSB PDB 6YHD · PDBe 6YHD · UniProt P28720
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