Research workbench
Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser
Analyse Two apo structures of the adenine riboswitch aptamer domain determined using an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E54
- 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
- MG
- Pockets
- 6 · best druggability 0.63
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
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.63 | 0.85 | 21 | empty |
| 2 | 231 | 0.60 | 0.82 | 28 | empty |
| 3 | 167 | 0.56 | 0.82 | 26 | empty |
| 4 | 136 | 0.55 | 0.83 | 17 | MG |
| 5 | 146 | 0.50 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 431 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Compared structures
- 5E54 · Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray… · 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 5E54 · PDBe 5E54
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