Research workbench
Speciation of a group I intron into a lariat capping ribozyme (circularly permutated ribozyme)
Analyse Speciation of a group I intron into a lariat capping ribozyme (circularly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P95
- Type
- RNA
- Length
- 189 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (192-mer)
- Ligands
- MG, NA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (192-mer) | rna | 189 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.75 | 0.79 | 51 | empty |
| 2 | 1141 | 0.69 | 0.75 | 48 | empty |
| 3 | 413 | 0.55 | 0.74 | 33 | empty |
| 4 | 76 | 0.27 | 0.72 | 12 | empty |
| 5 | 76 | 0.26 | 0.72 | 13 | empty |
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4P95 · PDBe 4P95
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