Research workbench
SAM-III riboswitch ON-state
Analyse SAM-III riboswitch ON-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C27
- Type
- RNA
- Length
- 94 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.601
- Molecule
- SAM-III riboswitch
- Ligands
- NCO
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · resolution 3.601 · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SAM-III riboswitch | rna | 47 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.59 | 0.74 | 32 | empty |
| 2 | 400 | 0.54 | 0.74 | 25 | NCO |
| 3 | 196 | 0.49 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 12 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6C27 · SAM-III riboswitch on-state · 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
- Elsewhere: RCSB PDB 6C27 · PDBe 6C27
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