MolNFT v1 · #121738 · protein
RNA editing tutase 1 from trypanosoma brucei in complex with UTP analog umpnpp
5I49 · 3' terminal uridylyl transferase: “RNA editing tutase 1 from trypanosoma brucei in complex with UTP analog umpnpp”. X-ray diffraction, 3 ligands (2KH, ZN, MG), 7 pockets (best druggability 0.64). MolNFT v1 #121738 on GenesisL1: 3D…
- PDB
- 5I49
- 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
- 2KH, ZN, MG
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3' terminal uridylyl transferase | protein | 471 | 46% helix, 13% strand | Q8WQX5 |
Ligands and binding sites
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.64 | 0.77 | 41 | 2KH, MG |
| 2 | 95 | 0.43 | 0.78 | 15 | empty |
| 3 | 90 | 0.42 | 0.78 | 19 | empty |
| 4 | 80 | 0.38 | 0.77 | 16 | empty |
| 5 | 89 | 0.37 | 0.76 | 17 | empty |
Compared structures
- 5I49 · RNA Editing TUTase 1 from Trypanosoma brucei in complex with UTP analog UMPNPP · 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 5I49 · PDBe 5I49 · UniProt Q8WQX5
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