Research workbench
Oceanobacillus iheyensis group II intron domain 1
Analyse Oceanobacillus iheyensis group II intron domain 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y1O
- Type
- RNA
- Length
- 514 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group II intron, domain 1
- Ligands
- MG, K
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group II intron, domain 1 | rna | 258 | — | — |
| B | Group II intron, domain 1 | rna | 256 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 19 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.66 | 0.75 | 33 | MG |
| 2 | 824 | 0.65 | 0.74 | 42 | MG |
| 3 | 732 | 0.65 | 0.75 | 36 | MG, K |
| 4 | 837 | 0.64 | 0.73 | 40 | MG |
| 5 | 358 | 0.63 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 155 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 4Y1O · Oceanobacillus iheyensis group II intron domain 1 · 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 4Y1O · PDBe 4Y1O
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