MolNFT v1 · #146578 · RNA
Prpp riboswitch bound to prpp, manganese chloride soaked structure
6DLQ: “Prpp riboswitch bound to prpp, manganese chloride soaked structure”. X-ray diffraction, 4 ligands (PRP, MN, NA), 3 pockets (best druggability 0.72). MolNFT v1 #146578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DLQ
- Type
- RNA
- Length
- 107 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prpp riboswitch
- Ligands
- PRP, MN, NA, K
- Pockets
- 3 · best druggability 0.72
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
- MN · Manganese (II) ion · metal · 12 copies · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- K · Potassium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.72 | 0.81 | 38 | PRP, MN |
| 2 | 906 | 0.69 | 0.76 | 52 | MN |
| 3 | 186 | 0.53 | 0.80 | 17 | NA |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6DLQ · PRPP Riboswitch bound to PRPP, manganese chloride soaked 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 6DLQ · PDBe 6DLQ
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