Research workbench
Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt 23S RNA from Thermus thermophilus
Analyse Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UMY
- Type
- protein + RNA
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Thermus thermophilus
- Molecule
- 50S ribosomal protein L1; RNA (80-mer)
- UniProt
- P27150
- Ligands
- MG, NA, SO4, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L1 | protein | 228 | 32% helix, 22% strand | P27150 |
| B | RNA (80-mer) | rna | 80 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B
- NA · Sodium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.81 | 0.83 | 76 | MG |
| 2 | 226 | 0.56 | 0.80 | 26 | MG |
| 3 | 79 | 0.39 | 0.78 | 20 | SO4 |
| 4 | 70 | 0.29 | 0.74 | 17 | empty |
| 5 | 55 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1652 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 3UMY · Crystal structure of mutant ribosomal protein T217A TTHL1 in complex with 80NT 23S RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P27150 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P27150) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P27150
- Elsewhere: RCSB PDB 3UMY · PDBe 3UMY · UniProt P27150
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.