MolNFT v1 · #188616 · protein + RNA
Crystal structure of pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6
7U0Y · Fab BL3-6 heavy chain: “Crystal structure of pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6”. X-ray diffraction, 2 ligands (KY6, MG), 7 pockets (best druggability 0.66). MolNFT v1 #188616 on GenesisL1: 3D structure…
- PDB
- 7U0Y
- Type
- protein + RNA
- Length
- 502 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab BL3-6 heavy chain; Fab BL3-6 light chain; RNA aptamer
- Ligands
- KY6, MG
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab BL3-6 heavy chain | protein | 223 | 3% helix, 52% strand | — |
| L | Fab BL3-6 light chain | protein | 212 | 7% helix, 51% strand | — |
| R | RNA aptamer | rna | 67 | — | — |
Ligands and binding sites
- KY6 · 4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile · ligand · chains R
- MG · Magnesium ion · metal · 2 copies · chains R
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 | 772 | 0.66 | 0.75 | 50 | empty |
| 2 | 332 | 0.56 | 0.76 | 48 | empty |
| 3 | 387 | 0.53 | 0.74 | 29 | empty |
| 4 | 118 | 0.39 | 0.75 | 24 | empty |
| 5 | 99 | 0.37 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1896 Ų buried · 14 hydrogen bonds · protein-protein
- H–R · 688 Ų buried · 17 hydrogen bonds · protein-nucleic
- L–R · 117 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 7U0Y · Crystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6 · 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 7U0Y · PDBe 7U0Y
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