MolNFT v1 · #177935 · RNA
Holo L-16 scai tetrahymena ribozyme
7EZ2 · Holo L-16 scai tetrahymena ribozyme S1: “Holo L-16 scai tetrahymena ribozyme”. Electron microscopy, 1 ligand (MG), 17 pockets (best druggability 0.78). MolNFT v1 #177935 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EZ2
- Type
- RNA
- Length
- 406 nucleotides
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo L-16 scai tetrahymena ribozyme S1; Holo L-16 scai tetrahymena ribozyme S2; Holo L-16…
- Ligands
- MG
- Pockets
- 17 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holo L-16 scai tetrahymena ribozyme S1 | rna | 8 | — | — |
| B | Holo L-16 scai tetrahymena ribozyme S2 | rna | 6 | — | — |
| N | Holo L-16 scai tetrahymena ribozyme | rna | 392 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 31 copies · chains N, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.78 | 0.81 | 65 | MG |
| 2 | 681 | 0.64 | 0.75 | 32 | empty |
| 3 | 423 | 0.64 | 0.79 | 31 | MG |
| 4 | 721 | 0.63 | 0.74 | 36 | MG |
| 5 | 577 | 0.60 | 0.74 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–N · 721 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- B–N · 454 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- A–B · 106 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7EZ2 · Holo L-16 ScaI Tetrahymena ribozyme · 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 7EZ2 · PDBe 7EZ2
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