Research workbench
Prpp riboswitch bound to prpp, native structure
Analyse Prpp riboswitch bound to prpp, native structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DLT
- Type
- RNA
- Length
- 107 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prpp riboswitch
- Ligands
- PRP, MG, NA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prpp riboswitch | rna | 107 | — | — |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
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 | 591 | 0.71 | 0.80 | 33 | MG, PRP |
| 2 | 887 | 0.69 | 0.76 | 53 | MG |
| 3 | 171 | 0.48 | 0.78 | 16 | empty |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6DLT · PRPP Riboswitch bound to PRPP, native structure · 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 6DLT · PDBe 6DLT
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