MolNFT v1 · #146135 · RNA
Group I self-splicing intron P4-P6 domain mutant U131A (without isopropanol soaking)
6D8L: “Group I self-splicing intron P4-P6 domain mutant U131A (without isopropanol soaking)”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.77). MolNFT v1 #146135 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6D8L
- Type
- RNA
- Length
- 316 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group I self-splicing intron
- Ligands
- MG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Group I self-splicing intron | rna | 158 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.77 | 0.85 | 43 | MG |
| 2 | 498 | 0.76 | 0.85 | 36 | empty |
| 3 | 445 | 0.74 | 0.85 | 43 | MG |
| 4 | 282 | 0.70 | 0.86 | 25 | MG |
| 5 | 466 | 0.55 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
- 6D8L · Group I self-splicing intron P4-P6 domain mutant U131A (without isopropanol soaking) · 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 6D8L · PDBe 6D8L
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