MolNFT v1 · #74444 · RNA
Crystal structure of glycine riboswitch, soaked in iridium
3OWZ · Domain II of glycine riboswitch: “Crystal structure of glycine riboswitch, soaked in iridium”. X-ray diffraction, 3 ligands (IRI, GLY, MG), 12 pockets (best druggability 0.64). MolNFT v1 #74444 on GenesisL1: 3D structure, binding…
- PDB
- 3OWZ
- Type
- RNA
- Length
- 171 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Domain II of glycine riboswitch
- Ligands
- IRI, GLY, MG
- Pockets
- 12 · 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 | 83 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 23 copies · chains A, B
- GLY · Glycine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.64 | 0.80 | 22 | MG, IRI |
| 2 | 263 | 0.63 | 0.82 | 24 | MG, IRI |
| 3 | 344 | 0.58 | 0.78 | 23 | MG, IRI |
| 4 | 270 | 0.48 | 0.74 | 17 | IRI |
| 5 | 163 | 0.47 | 0.78 | 24 | GLY, MG, IRI |
Interfaces
1 interface between chains.
- A–B · 1224 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 3OWZ · Crystal structure of glycine riboswitch, soaked in Iridium · 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 3OWZ · PDBe 3OWZ
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