Research workbench
Botulinum neurotoxin A4 cell binding domain in complex with GD1A oligosaccharide
Analyse Botulinum neurotoxin A4 cell binding domain in complex with GD1A oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QPT
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurotoxin type a
- UniProt
- Q3LRX8
- Ligands
- GAL, BGC, NGA, SIA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurotoxin type a | protein | 420 | 6% helix, 47% strand | Q3LRX8 |
| B | Neurotoxin type a | protein | 390 | 8% helix, 46% strand | Q3LRX8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, A
- BGC · beta-D-glucopyranose · sugar · 2 copies
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains B, A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.83 | 0.85 | 97 | empty |
| 2 | 309 | 0.69 | 0.83 | 38 | empty |
| 3 | 270 | 0.59 | 0.79 | 29 | empty |
| 4 | 70 | 0.36 | 0.77 | 14 | empty |
| 5 | 65 | 0.29 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7QPT · Botulinum neurotoxin A4 cell binding domain in complex with GD1a oligosaccharide · the same entry in another collection · chain A against A, 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
- Every structure of UniProt Q3LRX8
- Elsewhere: RCSB PDB 7QPT · PDBe 7QPT · UniProt Q3LRX8
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