MolNFT v1 · #4670 · protein + RNA
Partial structure of 16S RNA of the small ribosomal subunit from thermus thermophilus
1DV4 · 16S ribosomal RNA: “Partial structure of 16S RNA of the small ribosomal subunit from thermus thermophilus”. X-ray diffraction, 1 ligand (WO2), 1 pocket (best druggability 0.35). MolNFT v1 #4670 on GenesisL1: 3D structure, binding…
- PDB
- 1DV4
- Type
- protein + RNA
- Length
- 642 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; Ribosomal protein S5; Ribosomal protein S7
- UniProt
- P02357, P17291
- Ligands
- WO2
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 362 | — | — |
| E | Ribosomal protein S5 | protein | 145 | 0% helix, 0% strand | P02357 |
| G | Ribosomal protein S7 | protein | 135 | 0% helix, 0% strand | P17291 |
Ligands and binding sites
- WO2 · Octadecatungstenyl diphosphate · ligand · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.35 | 0.72 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–E · 106 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–G · 24 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 1DV4 · Partial structure of 16S RNA of the small ribosomal subunit from thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- P02357 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (P02357) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 P02357
- Every structure of UniProt P17291
- Elsewhere: RCSB PDB 1DV4 · PDBe 1DV4 · UniProt P02357 · UniProt P17291
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