Research workbench
A processed non-coding RNA regulates a bacterial antiviral system
Analyse A processed non-coding RNA regulates a bacterial antiviral system in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XD0
- Type
- protein + RNA
- Length
- 1,188 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxn; Toxi
- EC
- 3.1.27.3
- UniProt
- B8X8Z0
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, X, Y, Z | Toxn (EC 3.1.27.3) | protein | 162 | 36% helix, 25% strand | B8X8Z0 |
| G, H, I, U, V, W | Toxi | rna | 36 | — | — |
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.72 | 0.79 | 68 | empty |
| 2 | 383 | 0.67 | 0.81 | 39 | empty |
| 3 | 410 | 0.64 | 0.79 | 39 | empty |
| 4 | 192 | 0.58 | 0.81 | 24 | empty |
| 5 | 173 | 0.55 | 0.80 | 23 | empty |
Interfaces
24 interfaces between chains.
- U–Z · 1346 Ų buried · 34 hydrogen bonds · protein-nucleic
- E–G · 1336 Ų buried · 39 hydrogen bonds · protein-nucleic
- B–I · 1334 Ų buried · 36 hydrogen bonds · protein-nucleic
- V–X · 1330 Ų buried · 36 hydrogen bonds · protein-nucleic
- W–Y · 1322 Ų buried · 32 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 2XD0 · A processed non-coding RNA regulates a bacterial antiviral system · the same entry in another collection · chain Z against Z, 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 B8X8Z0
- Elsewhere: RCSB PDB 2XD0 · PDBe 2XD0 · UniProt B8X8Z0
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