MolNFT v1 · #117721 · protein
TRNA guanine transglycosylase (tgt) in complex with an immucillin derivative
5EGR · Queuine tRNA-ribosyltransferase: “TRNA guanine transglycosylase (tgt) in complex with an immucillin derivative”. X-ray diffraction, 2 ligands (5NT, ZN), 1 pocket (best druggability 0.48). MolNFT v1 #117721 on GenesisL1: 3D…
- PDB
- 5EGR
- 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
- 5NT, ZN
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 362 | 46% helix, 17% strand | P28720 |
Ligands and binding sites
- 5NT · 2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.48 | 0.78 | 21 | 5NT |
Compared structures
- 5EGR · tRNA guanine transglycosylase (TGT) in complex with an Immucillin derivative · 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 5EGR · PDBe 5EGR · UniProt P28720
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