Research workbench
Binding domain of BONT/A complexed with ganglioside variant
Analyse Binding domain of BONT/A complexed with ganglioside variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TPB
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type a
- EC
- 3.4.24.69
- UniProt
- P10845
- Ligands
- NGA, GAL, SIA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 411 | 5% helix, 47% strand | P10845 |
| B | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 407 | 6% helix, 46% strand | P10845 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains B
- GAL · beta-D-galactopyranose · sugar · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.76 | 0.80 | 75 | empty |
| 2 | 168 | 0.66 | 0.86 | 30 | empty |
| 3 | 524 | 0.62 | 0.75 | 59 | empty |
| 4 | 56 | 0.51 | 0.87 | 20 | empty |
| 5 | 155 | 0.48 | 0.77 | 29 | GAL, SIA |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5TPB · Binding domain of BoNT/A complexed with ganglioside variant · 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 P10845
- Elsewhere: RCSB PDB 5TPB · PDBe 5TPB · UniProt P10845
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