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Co-evolution of protein and RNA structures within a highly conserved ribosomal domain
Analyse Co-evolution of protein and RNA structures within a highly conserved ribosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y39
- Type
- protein + RNA
- Length
- 262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 58 nucleotide ribosomal 23S RNA domain; 50S ribosomal protein L11
- UniProt
- P56210
- Ligands
- MG, 3CO, K
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 58 nucleotide ribosomal 23S RNA domain | rna | 58 | — | — |
| A | 50S ribosomal protein L11 | protein | 74 | 45% helix, 8% strand | P56210 |
| B | 50S ribosomal protein L11 | protein | 72 | 44% helix, 11% strand | P56210 |
Ligands and binding sites
- MG · Magnesium ion · metal · 18 copies · chains C, D
- 3CO · Cobalt (III) ion · metal · 2 copies · chains C, D
- K · Potassium ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.69 | 0.75 | 55 | MG, 3CO |
| 2 | 248 | 0.65 | 0.84 | 23 | MG |
| 3 | 268 | 0.60 | 0.81 | 22 | MG |
| 4 | 94 | 0.36 | 0.76 | 14 | MG |
| 5 | 68 | 0.31 | 0.75 | 14 | MG |
Interfaces
4 interfaces between chains.
- D–B · 1044 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–A · 1011 Ų buried · 30 hydrogen bonds · protein-nucleic
- D–A · 85 Ų buried · 0 hydrogen bonds · protein-nucleic
- C–D · 52 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1Y39 · Co-evolution of protein and RNA structures within a highly conserved ribosomal domain · the same entry in another collection · chain C against C, TM-score 1.00
- P56210 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P56210) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P56210
- Elsewhere: RCSB PDB 1Y39 · PDBe 1Y39 · UniProt P56210
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