Research workbench
RNA-protein interactions: the crystal structure of ribosomal protein S8/RRNA complex from methanococcus jannaschii
Analyse RNA-protein interactions: the crystal structure of ribosomal protein S8/RRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I6U
- Type
- protein + RNA
- Length
- 330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA fragment; 30S ribosomal protein S8P
- UniProt
- P54041
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 16S rRNA fragment | rna | 37 | — | — |
| A | 30S ribosomal protein S8P | protein | 129 | 30% helix, 27% strand | P54041 |
| B | 30S ribosomal protein S8P | protein | 127 | 31% helix, 29% strand | P54041 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.64 | 0.77 | 35 | empty |
| 2 | 511 | 0.64 | 0.77 | 29 | empty |
| 3 | 217 | 0.58 | 0.80 | 23 | empty |
| 4 | 123 | 0.40 | 0.75 | 18 | empty |
| 5 | 55 | 0.33 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 912 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–B · 836 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–B · 309 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1I6U · RNA-protein interactions: the crystal structure of ribosomal protein S8/RRNA complex from… · the same entry in another collection · chain C against C, TM-score 1.00
- P54041 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P54041) · a predicted model of the same protein · chain B 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 P54041
- Elsewhere: RCSB PDB 1I6U · PDBe 1I6U · UniProt P54041
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