MolNFT v1 · #6288 · protein + RNA
The crystal structure of two uucg loops highlights the role played by 2'-hydroxyl groups in its unusual stability
1F7Y · 16S ribosomal RNA fragment: “The crystal structure of two uucg loops highlights the role played by 2'-hydroxyl groups in its unusual…”. X-ray diffraction, 3 ligands (MG, NA, K), 2 pockets (best druggability 0.69). MolNFT v1 #6288 on…
- PDB
- 1F7Y
- Type
- protein + RNA
- Length
- 143 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA fragment; 30S ribosomal protein S15
- UniProt
- P80378
- Ligands
- MG, NA, K
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 16S ribosomal RNA fragment | rna | 57 | — | — |
| A | 30S ribosomal protein S15 | protein | 86 | 71% helix, 0% strand | P80378 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains B
- NA · Sodium ion · metal · 2 copies · chains B
- K · Potassium ion · metal · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.69 | 0.76 | 42 | MG |
| 2 | 58 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 1264 Ų buried · 31 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1F7Y · The crystal structure of two uucg loops highlights the role played by 2'-hydroxyl groups… · the same entry in another collection · chain B against B, TM-score 1.00
- P80378 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (P80378) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P80378
- Elsewhere: RCSB PDB 1F7Y · PDBe 1F7Y · UniProt P80378
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