MolNFT v1 · #164624 · RNA
Structure of oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, MG2+ and 5'-exon
6T3R · Group iic intron ribozyme: “Structure of oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+…”. X-ray diffraction, 3 ligands (SPM, MG, K), 15 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 6T3R
- Type
- RNA
- Length
- 393 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
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group iic intron ribozyme | rna | 388 | — | — |
| B | Group iic intron ribozyme | rna | 5 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 30 copies · chains A, B
- K · Potassium ion · metal · 19 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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.77 | 0.81 | 58 | MG |
| 2 | 855 | 0.68 | 0.76 | 58 | MG, K |
| 3 | 425 | 0.68 | 0.81 | 40 | MG |
| 4 | 729 | 0.66 | 0.76 | 44 | MG, K |
| 5 | 776 | 0.63 | 0.73 | 34 | MG |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6T3R · Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) 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 6T3R · PDBe 6T3R
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