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Crystal structure of mutant ribosomal protein M218L TTHL1 in complex with 80NT 23S RNA from thermus thermophilus
Analyse Crystal structure of mutant ribosomal protein M218L 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
- 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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