MolNFT v1 · #146600 · RNA
Ppgpp riboswitch bound to ppgpp, thallium acetate structure
6DME: “Ppgpp riboswitch bound to ppgpp, thallium acetate structure”. X-ray diffraction, 3 ligands (G4P, MG, TL), 3 pockets (best druggability 0.66). MolNFT v1 #146600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DME
- Type
- RNA
- Length
- 102 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ppgpp riboswitch
- Ligands
- G4P, MG, TL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ppgpp riboswitch | rna | 102 | — | — |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · chains A
- MG · Magnesium ion · metal · 13 copies · chains A
- TL · Thallium (I) 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.66 | 0.76 | 42 | MG |
| 2 | 486 | 0.54 | 0.73 | 34 | G4P, MG |
| 3 | 169 | 0.43 | 0.75 | 14 | MG |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6DME · ppGpp Riboswitch bound to ppGpp, thallium acetate 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 6DME · PDBe 6DME
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