Research workbench
Crystal structure of glycine riboswitch, MN2+ soaked
Analyse Crystal structure of glycine riboswitch, MN2+ soaked in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OXE
- Type
- RNA
- Length
- 176 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Domain II of glycine riboswitch
- Ligands
- GLY, MN, MG
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Domain II of glycine riboswitch | rna | 88 | — | — |
| B | Domain II of glycine riboswitch | rna | 88 | — | — |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 32 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.64 | 0.82 | 24 | MN, MG |
| 2 | 414 | 0.62 | 0.78 | 22 | MN, MG |
| 3 | 342 | 0.61 | 0.79 | 24 | MN |
| 4 | 316 | 0.51 | 0.74 | 24 | MG |
| 5 | 295 | 0.48 | 0.73 | 25 | MN, MG |
Interfaces
1 interface between chains.
- A–B · 1233 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 3OXE · crystal structure of glycine riboswitch, Mn2+ soaked · 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 3OXE · PDBe 3OXE
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