MolNFT v1 · #122046 · protein
RNA editing tutase 1 from trypanosoma brucei in complex with UTP
5IDO · 3' terminal uridylyl transferase: “RNA editing tutase 1 from trypanosoma brucei in complex with UTP”. X-ray diffraction, 3 ligands (UTP, ZN, MG), 6 pockets (best druggability 0.63). MolNFT v1 #122046 on GenesisL1: 3D structure…
- PDB
- 5IDO
- Type
- protein
- Length
- 471 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3' terminal uridylyl transferase
- UniProt
- Q8WQX5
- Ligands
- UTP, ZN, MG
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3' terminal uridylyl transferase | protein | 471 | 47% helix, 13% strand | Q8WQX5 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.63 | 0.76 | 41 | UTP, MG |
| 2 | 161 | 0.49 | 0.77 | 32 | empty |
| 3 | 56 | 0.40 | 0.81 | 17 | empty |
| 4 | 99 | 0.40 | 0.77 | 19 | empty |
| 5 | 75 | 0.37 | 0.77 | 16 | empty |
Compared structures
- 5IDO · RNA Editing TUTase 1 from Trypanosoma brucei in complex with UTP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WQX5 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase 1 (Q8WQX5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8WQX5
- Elsewhere: RCSB PDB 5IDO · PDBe 5IDO · UniProt Q8WQX5
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