Research workbench
Crystal structure of fragment of ribosomal protein P0 in complex with 74NT 23S RNA from methanococcus jannaschii
Analyse Crystal structure of fragment of ribosomal protein P0 in complex with 74NT 23S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6G
- Type
- protein + RNA
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L10; 23S ribosomal RNA
- UniProt
- P54049
- Ligands
- MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L10 | protein | 205 | 34% helix, 18% strand | P54049 |
| 0 | 23S ribosomal RNA | rna | 74 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains 0
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.74 | 0.79 | 57 | empty |
| 2 | 542 | 0.71 | 0.80 | 69 | empty |
| 3 | 101 | 0.63 | 0.88 | 18 | empty |
| 4 | 113 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–0 · 1079 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 5D6G · Crystal structure of fragment of ribosomal protein P0 in complex with 74NT 23S RNA from… · the same entry in another collection · chain A against A, TM-score 1.00
- P54049 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L10 (P54049) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P54049
- Elsewhere: RCSB PDB 5D6G · PDBe 5D6G · UniProt P54049
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