MolNFT v1 · #128418 · protein + RNA
Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N- terminal residues in complex with 80NT 23S RNA from thermus thermophilus
5NPM · 50S ribosomal protein L1: “Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N- terminal residues in complex with 80NT 23S…”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.78). MolNFT v1 #128418 on…
- PDB
- 5NPM
- Type
- protein + RNA
- Length
- 291 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L1; 23S ribosomal RNA
- UniProt
- P27150
- Ligands
- NA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L1 | protein | 211 | 36% helix, 24% strand | P27150 |
| B | 23S ribosomal RNA | rna | 80 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.78 | 0.81 | 67 | empty |
| 2 | 78 | 0.31 | 0.75 | 19 | empty |
| 3 | 107 | 0.30 | 0.72 | 15 | empty |
| 4 | 53 | 0.22 | 0.72 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1058 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 5NPM · Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N-terminal residues in… · 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 0.99
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 5NPM · PDBe 5NPM · UniProt P27150
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