MolNFT v1 · #170781 · protein
TRNA-guanine transglycosylase (tgt) in co-crystallized complex (P2) with 6-amino-2-(methylamino)-4-phenethyl-1,7-dihydro-8H-IMIDAZO[4,5- G]QUINAZOLIN-8-one
6YIQ · Queuine tRNA-ribosyltransferase: “TRNA-guanine transglycosylase (tgt) in co-crystallized complex (P2) with…”. X-ray diffraction, 2 ligands (OQN, ZN), 3 pockets (best druggability 0.63). MolNFT v1 #170781 on GenesisL1: 3D structure…
- PDB
- 6YIQ
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Queuine tRNA-ribosyltransferase
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- OQN, ZN
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 359 | 46% helix, 18% strand | P28720 |
| B | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 366 | 47% helix, 18% strand | P28720 |
Ligands and binding sites
- OQN · 6-amino-2-(methylamino)-4-phenethyl-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.63 | 0.84 | 29 | OQN |
| 2 | 242 | 0.62 | 0.81 | 39 | OQN |
| 3 | 66 | 0.31 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 242 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6YIQ · tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex (P2) with… · the same entry in another collection · chain B against B, 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 6YIQ · PDBe 6YIQ · UniProt P28720
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