MolNFT v1 · #164617 · RNA
Structure of oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, MG2+ and 5'-exon
6T3K · Group iic intron ribozyme: “Structure of oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+…”. X-ray diffraction, 3 ligands (SPM, MG, K), 16 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 6T3K
- Type
- RNA
- Length
- 394 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group iic intron ribozyme
- Ligands
- SPM, MG, K
- Pockets
- 16 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group iic intron ribozyme | rna | 389 | — | — |
| B | Group iic intron ribozyme | rna | 5 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 28 copies · chains A, B
- K · Potassium ion · metal · 15 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.65 | 0.83 | 30 | MG |
| 2 | 670 | 0.65 | 0.76 | 55 | MG, K |
| 3 | 213 | 0.64 | 0.84 | 24 | MG |
| 4 | 329 | 0.63 | 0.80 | 38 | MG, K |
| 5 | 556 | 0.62 | 0.76 | 31 | MG, EPE |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 6T3K · Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the… · 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 6T3K · PDBe 6T3K
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