MolNFT v1 · #146225 · protein + RNA
Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2S RNA aptamer
6DB9 · RNA (60-mer): “Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2S RNA aptamer”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.70). MolNFT v1 #146225 on GenesisL1: 3D structure…
- PDB
- 6DB9
- Type
- protein + RNA
- Length
- 488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (60-mer); Fab-heavy-chain; Fab-light-chain
- Ligands
- MG
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA (60-mer) | rna | 60 | — | — |
| H | Fab-heavy-chain | protein | 219 | 10% helix, 51% strand | — |
| L | Fab-light-chain | protein | 209 | 5% helix, 48% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.70 | 0.78 | 59 | MG |
| 2 | 348 | 0.57 | 0.75 | 39 | empty |
| 3 | 181 | 0.50 | 0.77 | 34 | empty |
| 4 | 56 | 0.49 | 0.86 | 25 | empty |
| 5 | 200 | 0.46 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1898 Ų buried · 16 hydrogen bonds · protein-protein
- R–H · 752 Ų buried · 17 hydrogen bonds · protein-nucleic
- R–L · 139 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6DB9 · Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA… · the same entry in another collection · chain R against R, 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 6DB9 · PDBe 6DB9
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