Research workbench
Structure of a guanidine-I riboswitch from S. acidophilus
Analyse Structure of a guanidine-I riboswitch from S. acidophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T83
- Type
- RNA
- Length
- 89 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (95-mer)
- Ligands
- IRI, SPK, GAI, SR, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (95-mer) | rna | 89 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 3 copies · chains A
- SPK · Spermine (fully protonated form) · ligand · chains A
- GAI · Guanidine · ligand · chains A
- SR · Strontium ion · metal · 9 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.65 | 0.76 | 38 | SR, SPK, IRI |
| 2 | 184 | 0.47 | 0.76 | 16 | IRI |
| 3 | 163 | 0.41 | 0.74 | 15 | SR, IRI |
| 4 | 83 | 0.37 | 0.78 | 15 | SR |
Compared structures
- 5T83 · Structure of a guanidine-I riboswitch from S. acidophilus · 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 5T83 · PDBe 5T83
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