MolNFT v1 · #45905 · protein
Terminal uridylyl transferase 4 from trypanosoma brucei with bound dutp
2NOM · RNA uridylyl transferase: “Terminal uridylyl transferase 4 from trypanosoma brucei with bound dutp”. X-ray diffraction, 2 ligands (DUT, MG), 6 pockets (best druggability 0.78). MolNFT v1 #45905 on GenesisL1: 3D structure, binding…
- PDB
- 2NOM
- Type
- protein
- Length
- 580 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
- DUT, MG
- Pockets
- 6 · best druggability 0.78
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 | 325 | 45% helix, 12% strand | Q381M1 |
| B | RNA uridylyl transferase (EC 2.7.7.52) | protein | 255 | 45% helix, 9% strand | Q381M1 |
Ligands and binding sites
- DUT · Deoxyuridine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.78 | 0.82 | 79 | MG, DUT |
| 2 | 251 | 0.55 | 0.77 | 31 | empty |
| 3 | 269 | 0.53 | 0.76 | 29 | DUT |
| 4 | 111 | 0.47 | 0.80 | 22 | empty |
| 5 | 90 | 0.40 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 441 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2NOM · Terminal uridylyl transferase 4 from Trypanosoma brucei with bound dUTP · 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 0.98
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 2NOM · PDBe 2NOM · UniProt Q381M1
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