MolNFT v1 · #90089 · RNA
Structure of oceanobacillus iheyensis group II intron in the presence of K+, CA2+ and an oligonucleotide fragment substrate (low energy dataset)
4E8T · Group iic intron: “Structure of oceanobacillus iheyensis group II intron in the presence of K+, CA2+ and an oligonucleotide…”. X-ray diffraction, 3 ligands (SPM, CA, K), 15 pockets (best druggability 0.70). MolNFT v1 #90089 on…
- PDB
- 4E8T
- Type
- RNA
- Length
- 395 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group iic intron; 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3'
- Ligands
- SPM, CA, K
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group iic intron | rna | 387 | — | — |
| B | 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3' | rna | 8 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · 2 copies · chains A
- CA · Calcium ion · metal · 25 copies · chains A, B
- K · Potassium ion · metal · 14 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 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 | 424 | 0.70 | 0.83 | 32 | CA |
| 2 | 975 | 0.69 | 0.75 | 66 | K |
| 3 | 821 | 0.68 | 0.76 | 55 | CA, K, EPE |
| 4 | 631 | 0.62 | 0.74 | 33 | CA |
| 5 | 378 | 0.61 | 0.78 | 29 | CA, EPE |
Interfaces
1 interface between chains.
- A–B · 511 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 4E8T · Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an… · 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 4E8T · PDBe 4E8T
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