Research workbench
Archaeal exosome core
Analyse Archaeal exosome core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BA1
- Type
- protein
- Length
- 2,013 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archaeal exosome RNA binding protein CSL4; Archaeal exosome complex exonuclease RRP41…
- EC
- 3.1.13.-
- UniProt
- O30033, O29757, O29756
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Archaeal exosome RNA binding protein CSL4 | protein | 179 | 2% helix, 44% strand | O30033 |
| E, D, F | Archaeal exosome complex exonuclease RRP41 (EC 3.1.13.-) | protein | 245 | 33% helix, 35% strand | O29757 |
| H, G, I | Archaeal exosome complex exonuclease RRP42 (EC 3.1.13.-) | protein | 247 | 28% helix, 30% strand | O29756 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.77 | 0.81 | 81 | empty |
| 2 | 851 | 0.77 | 0.80 | 87 | empty |
| 3 | 966 | 0.75 | 0.78 | 84 | empty |
| 4 | 734 | 0.71 | 0.77 | 67 | empty |
| 5 | 1066 | 0.70 | 0.75 | 73 | empty |
Interfaces
18 interfaces between chains.
- F–I · 1573 Ų buried · 30 hydrogen bonds · protein-protein
- E–H · 1537 Ų buried · 27 hydrogen bonds · protein-protein
- D–G · 1520 Ų buried · 24 hydrogen bonds · protein-protein
- D–I · 1207 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1175 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2BA1 · Archaeal exosome core · the same entry in another collection · chain I against I, TM-score 1.00
- O29757 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (O29757) · a predicted model of the same protein · chain E against A, TM-score 1.00
- O29756 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (O29756) · a predicted model of the same protein · chain H against A, TM-score 0.99
- O30033 · AlphaFold monomer V2.0 prediction for exosome complex component CSL4 (O30033) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 O30033
- Every structure of UniProt O29757
- Every structure of UniProt O29756
- Elsewhere: RCSB PDB 2BA1 · PDBe 2BA1 · UniProt O30033 · UniProt O29757 · UniProt O29756
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