Research workbench
Structure and function of the polymerase core of tramp, a RNA surveillance complex
Analyse Structure and function of the polymerase core of tramp, a RNA surveillance… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NYB
- Type
- protein
- Length
- 387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) RNA polymerase protein 2; Protein AIR2
- EC
- 2.7.7.-
- UniProt
- P53632, Q12476
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(A) RNA polymerase protein 2 (EC 2.7.7.-) | protein | 323 | 46% helix, 14% strand | P53632 |
| B | Protein AIR2 | protein | 64 | 14% helix, 5% strand | Q12476 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.73 | 0.81 | 64 | empty |
| 2 | 64 | 0.45 | 0.83 | 21 | empty |
| 3 | 110 | 0.42 | 0.76 | 18 | empty |
| 4 | 85 | 0.41 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3NYB · Structure and function of the polymerase core of TRAMP, a RNA surveillance complex · the same entry in another collection · chain A against A, TM-score 1.00
- P53632 · AlphaFold monomer V2.0 prediction for POLY(A) RNA polymerase protein 2 (P53632) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q12476 · AlphaFold monomer V2.0 prediction for protein AIR2 (Q12476) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P53632
- Every structure of UniProt Q12476
- Elsewhere: RCSB PDB 3NYB · PDBe 3NYB · UniProt P53632 · UniProt Q12476
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.