Research workbench
Terminal uridylyl transferase 4 from trypanosoma brucei with bound UTP and ump
Analyse Terminal uridylyl transferase 4 from trypanosoma brucei with bound UTP and ump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q0F
- Type
- protein
- Length
- 642 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
- U5P, UTP, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA uridylyl transferase (EC 2.7.7.52) | protein | 324 | 45% helix, 12% strand | Q381M1 |
| B | RNA uridylyl transferase (EC 2.7.7.52) | protein | 318 | 45% helix, 11% strand | Q381M1 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- UTP · Uridine 5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.75 | 0.81 | 44 | MG, UTP, U5P |
| 2 | 503 | 0.64 | 0.76 | 48 | U5P |
| 3 | 386 | 0.60 | 0.76 | 57 | empty |
| 4 | 58 | 0.36 | 0.78 | 17 | empty |
| 5 | 54 | 0.33 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 470 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2Q0F · Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UMP · 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 0.96
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 2Q0F · PDBe 2Q0F · UniProt Q381M1
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