MolNFT v1 · #146224 · protein + RNA
Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2S RNA aptamer
6DB8 · Fab-heavy chain: “Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2S RNA aptamer”. X-ray diffraction, 1 ligand (G4A), 5 pockets (best druggability 0.71). MolNFT v1 #146224 on GenesisL1: 3D…
- PDB
- 6DB8
- Type
- protein + RNA
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab-heavy chain; RNA (60-mer); Fab-light chain
- Ligands
- G4A
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab-heavy chain | protein | 224 | 8% helix, 50% strand | — |
| R | RNA (60-mer) | rna | 60 | — | — |
| L | Fab-light chain | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- G4A · 2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.71 | 0.77 | 60 | empty |
| 2 | 511 | 0.59 | 0.74 | 58 | empty |
| 3 | 230 | 0.54 | 0.77 | 35 | empty |
| 4 | 76 | 0.32 | 0.74 | 15 | empty |
| 5 | 63 | 0.24 | 0.72 | 11 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1920 Ų buried · 20 hydrogen bonds · protein-protein
- H–R · 746 Ų buried · 20 hydrogen bonds · protein-nucleic
- R–L · 182 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6DB8 · Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA… · the same entry in another collection · chain H against H, 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 6DB8 · PDBe 6DB8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.