Research workbench
Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'- deoxyguanosine
Analyse Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SKI
- Type
- RNA
- Length
- 136 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (68-mer)
- Ligands
- GNG, MG, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (68-mer) | rna | 68 | — | — |
| B | RNA (68-mer) | rna | 68 | — | — |
Ligands and binding sites
- GNG · 2'-deoxy-guanosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- SIN · Succinic acid · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.71 | 0.78 | 47 | SO4 |
| 2 | 844 | 0.71 | 0.77 | 54 | SO4 |
| 3 | 137 | 0.59 | 0.85 | 19 | GNG |
| 4 | 193 | 0.56 | 0.80 | 22 | GNG |
Interfaces
1 interface between chains.
- A–B · 388 Ų buried · 20 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 3SKI · Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine · 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 3SKI · PDBe 3SKI
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