MolNFT v1 · #57254 · protein
The structure of archaeal ribosomal stalk P1/P0 complex
3A1Y · 50S ribosomal protein P1 (L12P): “The structure of archaeal ribosomal stalk P1/P0 complex”. X-ray diffraction, 4 pockets (best druggability 0.66). MolNFT v1 #57254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A1Y
- Type
- protein
- Length
- 559 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein P1 (L12P); Acidic ribosomal protein P0
- UniProt
- O57705, O74109
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 50S ribosomal protein P1 (L12P) | protein | 58 | 69% helix, 0% strand | O57705 |
| G | Acidic ribosomal protein P0 | protein | 211 | 47% helix, 13% strand | O74109 |
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 | 627 | 0.66 | 0.76 | 74 | empty |
| 2 | 251 | 0.55 | 0.77 | 31 | empty |
| 3 | 72 | 0.34 | 0.75 | 13 | empty |
| 4 | 51 | 0.24 | 0.72 | 15 | empty |
Interfaces
12 interfaces between chains.
- F–G · 924 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 738 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 711 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 688 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 683 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3A1Y · The structure of archaeal ribosomal stalk P1/P0 complex · the same entry in another collection · chain G against G, TM-score 1.00
- O57705 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L12 (O57705) · a predicted model of the same protein · chain A against A, TM-score 0.97
- O74109 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L10 (O74109) · a predicted model of the same protein · chain G against A, TM-score 0.89
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 O57705
- Every structure of UniProt O74109
- Elsewhere: RCSB PDB 3A1Y · PDBe 3A1Y · UniProt O57705 · UniProt O74109
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