MolNFT v1 · #125998 · protein
TRNA guanine transglycosylase (tgt) in co-crystallized complex (space group C2) with 6-amino-4-(2-((3AR,4R,6R,6AR)-6-methoxy-2,2- DIMETHYLTETRAHYDROFURO[3,4-D][1,3]DIOXOL-4-YL)ETHYL)-2-(methylamino)- 1H-IMIDAZO[4,5-G]QUINAZOLIN-8(7H)-one
5LPP · Queuine tRNA-ribosyltransferase: “TRNA guanine transglycosylase (tgt) in co-crystallized complex (space group C2) with…”. X-ray diffraction, 2 ligands (72C, ZN), 3 pockets (best druggability 0.60). MolNFT v1 #125998 on GenesisL1: 3D…
- PDB
- 5LPP
- Type
- protein
- Length
- 340 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
- 72C, ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 340 | 46% helix, 18% strand | P28720 |
Ligands and binding sites
- 72C · 4-[2-[(3~{A}~{R},4~{R},6~{R},6~{A}~{R})-4-methoxy-2,2-dimethyl-3~{A},4,6,6~{A}-tetrahydrofuro[3,4-D][1, 3]dioxol-6-yl]ethyl]-6-azanyl-2-(methylamino)-1,7-dihydroimidazo[4,5-g]quinazolin-8-one · ligand · chains A
- ZN · Zinc ion · metal · 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 | 274 | 0.60 | 0.79 | 33 | 72C |
| 2 | 65 | 0.34 | 0.76 | 16 | empty |
| 3 | 53 | 0.28 | 0.75 | 13 | empty |
Compared structures
- 5LPP · tRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group C2) 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 5LPP · PDBe 5LPP · UniProt P28720
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