Research workbench
Terminal uridylyl transferase 4 from trypanosoma brucei with bound ATP
Analyse Terminal uridylyl transferase 4 from trypanosoma brucei with bound ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q0D
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA uridylyl transferase
- EC
- 2.7.7.52
- UniProt
- Q381M1
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA uridylyl transferase (EC 2.7.7.52) | protein | 325 | 47% helix, 13% strand | Q381M1 |
| B | RNA uridylyl transferase (EC 2.7.7.52) | protein | 323 | 48% helix, 11% strand | Q381M1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.75 | 0.82 | 51 | MG, ATP |
| 2 | 534 | 0.64 | 0.76 | 56 | empty |
| 3 | 166 | 0.50 | 0.78 | 26 | empty |
| 4 | 164 | 0.44 | 0.75 | 26 | empty |
| 5 | 88 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2Q0D · Terminal uridylyl transferase 4 from Trypanosoma brucei with bound ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q381M1 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase 4 (Q381M1) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q381M1
- Elsewhere: RCSB PDB 2Q0D · PDBe 2Q0D · UniProt Q381M1
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