Research workbench
Botulinum neurotoxin A5 cell binding domain in complex with GM1B oligosaccharide
Analyse Botulinum neurotoxin A5 cell binding domain in complex with GM1B oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QPU
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin sub-type A5
- EC
- 3.4.24.69
- UniProt
- C1IPK2
- Ligands
- GAL, SIA, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin sub-type A5 (EC 3.4.24.69) | protein | 387 | 5% helix, 45% strand | C1IPK2 |
| B | Botulinum neurotoxin sub-type A5 (EC 3.4.24.69) | protein | 351 | 5% helix, 45% strand | C1IPK2 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- SO4 · Sulfate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.81 | 0.84 | 65 | empty |
| 2 | 269 | 0.55 | 0.77 | 27 | empty |
| 3 | 283 | 0.54 | 0.76 | 28 | empty |
| 4 | 76 | 0.52 | 0.85 | 20 | empty |
| 5 | 73 | 0.45 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 746 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 7QPU · Botulinum neurotoxin A5 cell binding domain in complex with GM1b 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 C1IPK2
- Elsewhere: RCSB PDB 7QPU · PDBe 7QPU · UniProt C1IPK2
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