Research workbench
Terminal uridylyl transferase 4 from trypanosoma brucei with bound upu
Analyse Terminal uridylyl transferase 4 from trypanosoma brucei with bound upu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q0G
- Type
- protein
- Length
- 649 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
- UPU, MG, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA uridylyl transferase (EC 2.7.7.52) | protein | 325 | 45% helix, 12% strand | Q381M1 |
| B | RNA uridylyl transferase (EC 2.7.7.52) | protein | 324 | 44% helix, 11% strand | Q381M1 |
Ligands and binding sites
- UPU · [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S, 4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl hydrogen (S)-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.76 | 0.81 | 54 | MG, UPU |
| 2 | 851 | 0.76 | 0.80 | 62 | MG, UPU |
| 3 | 222 | 0.52 | 0.76 | 32 | empty |
| 4 | 152 | 0.48 | 0.77 | 27 | empty |
| 5 | 65 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 446 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2Q0G · Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UPU · 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 2Q0G · PDBe 2Q0G · UniProt Q381M1
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