MolNFT v1 · #21117 · protein + RNA
The structure of a ribosomal protein S8/SPC operon mRNA complex
1S03 · 47-mer: “The structure of a ribosomal protein S8/SPC operon mRNA complex”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.67). MolNFT v1 #21117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1S03
- Type
- protein + RNA
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 47-mer; 30S ribosomal protein S8
- UniProt
- P0A7W7
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 47-mer | rna | 47 | — | — |
| H | 30S ribosomal protein S8 | protein | 127 | 28% helix, 35% strand | P0A7W7 |
| G | 30S ribosomal protein S8 | protein | 126 | 29% helix, 34% strand | P0A7W7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 17 copies · chains A, H, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.67 | 0.78 | 32 | ZN |
| 2 | 505 | 0.66 | 0.78 | 34 | ZN |
| 3 | 435 | 0.56 | 0.74 | 28 | ZN |
| 4 | 339 | 0.49 | 0.73 | 28 | ZN |
| 5 | 79 | 0.40 | 0.78 | 11 | empty |
Interfaces
2 interfaces between chains.
- B–G · 931 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–H · 893 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 1S03 · The Structure of a Ribosomal Protein S8/spc Operon mRNA Complex · the same entry in another collection · chain A against A, TM-score 1.00
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 P0A7W7
- Elsewhere: RCSB PDB 1S03 · PDBe 1S03 · UniProt P0A7W7
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