Research workbench
Crystal structure of ribosomal protein TTHL1 in complex with 80NT 23S RNA from thermus thermophilus
Analyse Crystal structure of ribosomal protein TTHL1 in complex with 80NT 23S RNA from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U4M
- 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
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L1 | protein | 228 | 36% helix, 23% strand | P27150 |
| B | RNA (80-mer) | rna | 80 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- MLI · Malonate ion · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.76 | 0.79 | 76 | MLI, SO4, MG |
| 2 | 401 | 0.55 | 0.74 | 31 | empty |
| 3 | 73 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1433 Ų buried · 31 hydrogen bonds · protein-nucleic
Compared structures
- 3U4M · Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus… · 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 0.98
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 3U4M · PDBe 3U4M · UniProt P27150
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