Research workbench
TRNA guanine transglycosylase (tgt) in co-crystallized complex with 6- amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5- trimethoxytetrahydrofuran-2-YL)ETHYL)-1H-IMIDAZO[4,5-G]QUINAZOLIN- 8(7H)-one
Analyse TRNA guanine transglycosylase (tgt) in co-crystallized complex with 6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LPO
- Type
- protein
- Length
- 362 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
- 725, ZN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 362 | 45% helix, 17% strand | P28720 |
Ligands and binding sites
- 725 · 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.64 | 0.82 | 36 | 725 |
| 2 | 57 | 0.38 | 0.79 | 16 | empty |
| 3 | 94 | 0.34 | 0.74 | 18 | empty |
| 4 | 63 | 0.32 | 0.76 | 18 | EDO |
Compared structures
- 5LPO · tRNA guanine Transglycosylase (TGT) in co-crystallized complex with… · 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 5LPO · PDBe 5LPO · UniProt P28720
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