MolNFT v1 · #187872 · protein + RNA
Crystal structure of pepper RNA aptamer in complex with hbc ligand and Fab BL3-6
7SZU: “Crystal structure of pepper RNA aptamer in complex with hbc ligand and Fab BL3-6”. X-ray diffraction, 3 ligands (J8F, MG, NA), 8 pockets (best druggability 0.67). MolNFT v1 #187872 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7SZU
- Type
- protein + RNA
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA aptamer; BL3-6 Fab heavy chain; BL3-6 Fab light chain
- Ligands
- J8F, MG, NA
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA aptamer | rna | 67 | — | — |
| H | BL3-6 Fab heavy chain | protein | 224 | 7% helix, 50% strand | — |
| L | BL3-6 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- J8F · 4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl) amino]phenyl]ethenyl]benzenecarbonitrile · ligand · chains R
- MG · Magnesium ion · metal · 2 copies · chains R
- NA · Sodium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.67 | 0.75 | 50 | NA |
| 2 | 564 | 0.61 | 0.75 | 30 | empty |
| 3 | 232 | 0.59 | 0.80 | 39 | empty |
| 4 | 253 | 0.51 | 0.75 | 33 | empty |
| 5 | 56 | 0.50 | 0.87 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1876 Ų buried · 12 hydrogen bonds · protein-protein
- R–H · 679 Ų buried · 16 hydrogen bonds · protein-nucleic
- R–L · 121 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 7SZU · Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6 · 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 7SZU · PDBe 7SZU
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