MolNFT v1 · #105131 · protein + RNA
Crystal structure of mutant ribosomal protein M218L TTHL1 in complex with 80NT 23S RNA from thermus thermophilus
4QVI · 50S ribosomal protein L1: “Crystal structure of mutant ribosomal protein M218L TTHL1 in complex with 80NT 23S RNA from thermus…”. X-ray diffraction, 3 ligands (GLC, FRU, SO4), 4 pockets (best druggability 0.78). MolNFT v1 #105131 on…
- PDB
- 4QVI
- Type
- protein + RNA
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L1; Fragment of 23S rRNA
- UniProt
- P27150
- Ligands
- GLC, FRU, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L1 | protein | 229 | 37% helix, 22% strand | P27150 |
| B | Fragment of 23S rRNA | rna | 80 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.78 | 0.81 | 69 | GLC, FRU |
| 2 | 125 | 0.51 | 0.81 | 18 | empty |
| 3 | 89 | 0.31 | 0.74 | 16 | MES |
| 4 | 52 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1481 Ų buried · 27 hydrogen bonds · protein-nucleic
Compared structures
- 4QVI · Crystal structure of mutant ribosomal protein M218L 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 0.96
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 P27150
- Elsewhere: RCSB PDB 4QVI · PDBe 4QVI · UniProt P27150
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