Research workbench
Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2S RNA aptamer
Analyse Structural basis for promiscuous binding and activation of fluorogenic dyes by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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