Research workbench
Ppgpp riboswitch bound to ppgpp, manganese chloride structure
Analyse Ppgpp riboswitch bound to ppgpp, manganese chloride structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DMD
- Type
- RNA
- Length
- 204 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ppgpp riboswitch
- Ligands
- G4P, MN, NA, MG, K
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ppgpp riboswitch | rna | 102 | — | — |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 10 copies · chains A, B
- NA · Sodium ion · metal · 8 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.64 | 0.76 | 35 | NA |
| 2 | 560 | 0.62 | 0.75 | 31 | NA |
| 3 | 678 | 0.61 | 0.73 | 35 | G4P, MN, MG |
| 4 | 504 | 0.54 | 0.72 | 35 | G4P, MN, MG |
| 5 | 261 | 0.48 | 0.74 | 17 | NA |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 11 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6DMD · ppGpp Riboswitch bound to ppGpp, manganese chloride structure · the same entry in another collection · chain B against B, 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 6DMD · PDBe 6DMD
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