Research workbench
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex
Analyse Detailed analysis of RNA-protein interactions within the bacterial ribosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MJI
- Type
- protein + RNA
- Length
- 427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5S rRNA fragment; 50S ribosomal protein L5
- UniProt
- P41201
- Ligands
- MG, K
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5S rRNA fragment | rna | 34 | — | — |
| A | 50S ribosomal protein L5 | protein | 180 | 34% helix, 23% strand | P41201 |
| B | 50S ribosomal protein L5 | protein | 179 | 32% helix, 22% strand | P41201 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, D, A, B
- K · Potassium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.72 | 0.86 | 33 | K |
| 2 | 263 | 0.69 | 0.86 | 30 | K |
| 3 | 130 | 0.59 | 0.85 | 26 | empty |
| 4 | 117 | 0.57 | 0.84 | 25 | empty |
| 5 | 69 | 0.52 | 0.86 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–A · 906 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–B · 872 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–A · 571 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–B · 568 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 373 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1MJI · Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein… · the same entry in another collection · chain C against C, TM-score 1.00
- P41201 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L5 (P41201) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P41201
- Elsewhere: RCSB PDB 1MJI · PDBe 1MJI · UniProt P41201
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