Research workbench
Partial structure of 16S RNA of the small ribosomal subunit from thermus thermophilus
Analyse Partial structure of 16S RNA of the small ribosomal subunit from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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