Research workbench
Crystal structure of T3C mutant S15 ribosomal protein in complex with 16S rRNA
Analyse Crystal structure of T3C mutant S15 ribosomal protein in complex with 16S rRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KUQ
- Type
- protein + RNA
- Length
- 141 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA fragment; 30S ribosomal protein S15
- UniProt
- P80378
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 16S ribosomal RNA fragment | rna | 57 | — | — |
| A | 30S ribosomal protein S15 | protein | 84 | 70% helix, 0% strand | P80378 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.66 | 0.75 | 38 | empty |
| 2 | 94 | 0.36 | 0.75 | 9 | empty |
| 3 | 55 | 0.28 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1250 Ų buried · 32 hydrogen bonds · protein-nucleic
Compared structures
- 1KUQ · Crystal structure of T3C mutant S15 ribosomal protein in complex with 16S rRNA · the same entry in another collection · chain B against B, TM-score 1.00
- P80378 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (P80378) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P80378
- Elsewhere: RCSB PDB 1KUQ · PDBe 1KUQ · UniProt P80378
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