MolNFT v1 · #81313 · protein + RNA
Crystal structure of mutant ribosomal protein T217A TTHL1 in complex with 80NT 23S RNA from thermus thermophilus
3UMY · 50S ribosomal protein L1: “Crystal structure of mutant ribosomal protein T217A TTHL1 in complex with 80NT 23S RNA from thermus…”. X-ray diffraction, 4 ligands (MG, NA, SO4), 5 pockets (best druggability 0.81). MolNFT v1 #81313 on…
- PDB
- 3UMY
- Type
- protein + RNA
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
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