Research workbench
Structure of the adenine riboswitch aptamer domain in an intermediate- bound state
Analyse Structure of the adenine riboswitch aptamer domain in an intermediate- bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SWD
- Type
- RNA
- Length
- 133 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
- Ligands
- ADE, MG
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain | rna | 65 | — | — |
| B | Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain | rna | 68 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.68 | 0.83 | 37 | MG |
| 2 | 207 | 0.63 | 0.84 | 25 | empty |
| 3 | 183 | 0.54 | 0.80 | 17 | empty |
| 4 | 159 | 0.54 | 0.81 | 22 | empty |
| 5 | 52 | 0.32 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 425 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5SWD · Structure of the adenine riboswitch aptamer domain in an intermediate-bound 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 5SWD · PDBe 5SWD
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