Research workbench
Group I self-splicing intron P4-P6 domain mutant A125U/G126U
Analyse Group I self-splicing intron P4-P6 domain mutant A125U/G126U in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D8M
- Type
- RNA
- Length
- 317 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group I self-splicing intron
- Ligands
- MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group I self-splicing intron | rna | 158 | — | — |
| B | Group I self-splicing intron | rna | 159 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 23 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.80 | 0.83 | 52 | MG |
| 2 | 482 | 0.75 | 0.85 | 43 | empty |
| 3 | 448 | 0.75 | 0.85 | 43 | MG |
| 4 | 272 | 0.69 | 0.86 | 23 | MG |
| 5 | 632 | 0.62 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 963 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 6D8M · Group I self-splicing intron P4-P6 domain mutant A125U/G126U · 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 6D8M · PDBe 6D8M
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