MolNFT v1 · #121598 · protein
TRNA guanine transglycosylase (tgt) in co-crystallized complex with 6- amino-4-(2-phenylethyl)-1,7-dihydro-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-one
5I07 · Queuine tRNA-ribosyltransferase: “TRNA guanine transglycosylase (tgt) in co-crystallized complex with 6…”. X-ray diffraction, 2 ligands (NE8, ZN), 4 pockets (best druggability 0.76). MolNFT v1 #121598 on GenesisL1: 3D structure…
- PDB
- 5I07
- Type
- protein
- Length
- 736 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
- NE8, ZN
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 368 | 45% helix, 18% strand | P28720 |
Ligands and binding sites
- NE8 · 6-amino-4-(2-phenylethyl)-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 · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.76 | 0.80 | 84 | GOL, NE8 |
| 2 | 587 | 0.73 | 0.81 | 67 | GOL, NE8 |
| 3 | 56 | 0.31 | 0.77 | 12 | empty |
| 4 | 50 | 0.30 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1677 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5I07 · 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 5I07 · PDBe 5I07 · UniProt P28720
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