Research workbench
RNA structure
Analyse RNA structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GXY
- Type
- RNA
- Length
- 162 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylcobalamin riboswitch
- Ligands
- IRI, B1Z, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylcobalamin riboswitch | rna | 162 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 7 copies · chains A
- B1Z · Adenosylcobalamin · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.66 | 0.74 | 59 | B1Z, IRI |
| 2 | 523 | 0.60 | 0.75 | 29 | empty |
| 3 | 189 | 0.47 | 0.76 | 20 | empty |
| 4 | 120 | 0.36 | 0.74 | 11 | IRI |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4GXY · RNA structure · 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 4GXY · PDBe 4GXY
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