Research workbench
Crystal structure of glycine riboswitch with two mutations
Analyse Crystal structure of glycine riboswitch with two mutations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OXD
- Type
- RNA
- Length
- 175 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Domain II of glycine riboswitch
- Ligands
- MG
- Pockets
- 9 · best druggability 0.69
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 | 87 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 34 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 | 528 | 0.69 | 0.80 | 38 | MG |
| 2 | 448 | 0.62 | 0.77 | 25 | MG |
| 3 | 413 | 0.61 | 0.78 | 22 | MG |
| 4 | 360 | 0.52 | 0.74 | 24 | MG |
| 5 | 300 | 0.48 | 0.74 | 25 | MG |
Interfaces
1 interface between chains.
- A–B · 1241 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 3OXD · Crystal structure of glycine riboswitch with two mutations · 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 3OXD · PDBe 3OXD
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