MolNFT v1 · #122789 · RNA
Structure of the lariat form of a chimeric derivative of the oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.
5J02 · Group II intron lariat: “Structure of the lariat form of a chimeric derivative of the oceanobacillus iheyensis group II intron in the…”. X-ray diffraction, 2 ligands (MG, NH4), 18 pockets (best druggability 0.75). MolNFT v1 #122789…
- PDB
- 5J02
- Type
- RNA
- Length
- 421 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group II intron lariat; 5' exon analog (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3')
- Ligands
- MG, NH4
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group II intron lariat | rna | 414 | — | — |
| B | 5' exon analog (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3') | rna | 7 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.75 | 0.81 | 66 | MG |
| 2 | 581 | 0.71 | 0.81 | 39 | MG |
| 3 | 1079 | 0.71 | 0.76 | 59 | MG, NH4 |
| 4 | 453 | 0.68 | 0.81 | 26 | MG |
| 5 | 502 | 0.67 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 598 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5J02 · Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis… · the same entry in another collection · chain B against B, 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 5J02 · PDBe 5J02
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