Research workbench
Structural basis for the activity of a cytoplasmic RNA terminal U- transferase
Analyse Structural basis for the activity of a cytoplasmic RNA terminal U- transferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E80
- Type
- protein
- Length
- 1,282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) RNA polymerase protein CID1
- EC
- 2.7.7.-
- UniProt
- O13833
- Ligands
- UTP
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 317 | 46% helix, 14% strand | O13833 |
| B | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 311 | 47% helix, 14% strand | O13833 |
| C | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 330 | 43% helix, 15% strand | O13833 |
| D | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 324 | 44% helix, 14% strand | O13833 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.80 | 0.81 | 104 | empty |
| 2 | 473 | 0.72 | 0.82 | 46 | empty |
| 3 | 704 | 0.66 | 0.75 | 52 | UTP |
| 4 | 560 | 0.64 | 0.75 | 58 | UTP |
| 5 | 494 | 0.62 | 0.76 | 52 | UTP |
Interfaces
4 interfaces between chains.
- B–D · 737 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 276 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 104 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4E80 · Structural Basis for the Activity of a Cytoplasmic RNA Terminal U-transferase · the same entry in another collection · chain D against D, TM-score 1.00
- O13833 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase CID1 (O13833) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O13833
- Elsewhere: RCSB PDB 4E80 · PDBe 4E80 · UniProt O13833
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