MolNFT v1 · #121593 · protein
TRNA guanine transglycosylase (tgt) in co-crystallized complex with 6- amino-4-{2-[(CYCLOHEXYLMETHYL)AMINO]ETHYL}-2-(methylamino)-1,7- dihydro-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-one
5I02 · Queuine tRNA-ribosyltransferase: “TRNA guanine transglycosylase (tgt) in co-crystallized complex with 6…”. X-ray diffraction, 3 ligands (PK2, ZN, CL), 3 pockets (best druggability 0.63). MolNFT v1 #121593 on GenesisL1: 3D structure…
- PDB
- 5I02
- Type
- protein
- Length
- 356 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
- PK2, ZN, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 356 | 47% helix, 17% strand | P28720 |
Ligands and binding sites
- PK2 · 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.63 | 0.82 | 41 | PK2, CL |
| 2 | 72 | 0.37 | 0.78 | 19 | GOL |
| 3 | 65 | 0.31 | 0.75 | 14 | empty |
Compared structures
- 5I02 · 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 5I02 · PDBe 5I02 · UniProt P28720
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