Research workbench
Terminal uridylyl transferase 4 from trypanosoma brucei with bound UTP and upu
Analyse Terminal uridylyl transferase 4 from trypanosoma brucei with bound UTP and upu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KAL
- Type
- protein + RNA
- Length
- 645 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA uridylyltransferase 4; RNA (5'-R(*UP*U)-3')
- UniProt
- A4UBD5
- Ligands
- UTP, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA uridylyltransferase 4 | protein | 325 | 46% helix, 12% strand | A4UBD5 |
| B | RNA uridylyltransferase 4 | protein | 316 | 49% helix, 11% strand | A4UBD5 |
| Y, Z | RNA (5'-R(*UP*U)-3') | rna | 2 | — | — |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, Y, B, Z
- MG · Magnesium ion · metal · 5 copies · chains A, B, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.74 | 0.84 | 45 | UTP, MG |
| 2 | 431 | 0.73 | 0.83 | 44 | UTP, MG |
| 3 | 239 | 0.54 | 0.77 | 27 | empty |
| 4 | 124 | 0.41 | 0.75 | 21 | empty |
| 5 | 80 | 0.37 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 391 Ų buried · 9 hydrogen bonds · protein-protein
- A–Y · 380 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–Z · 357 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5KAL · Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UpU · the same entry in another collection · chain A against A, TM-score 1.00
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 A4UBD5
- Elsewhere: RCSB PDB 5KAL · PDBe 5KAL · UniProt A4UBD5
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