MolNFT v1 · #52215 · protein
Crystal structure of botulinum neurotoxin serotype a binding domain in complex with GT1B
2VU9 · Botulinum neurotoxin a heavy chain: “Crystal structure of botulinum neurotoxin serotype a binding domain in complex with GT1B”. X-ray diffraction, 5 ligands (GAL, SIA, BGC), 5 pockets (best druggability 0.54). MolNFT v1 #52215 on…
- PDB
- 2VU9
- Type
- protein
- Length
- 425 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a heavy chain
- EC
- 3.4.24.69
- UniProt
- P10845
- Ligands
- GAL, SIA, BGC, NGA, MG
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a heavy chain (EC 3.4.24.69) | protein | 425 | 7% helix, 45% strand | P10845 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.54 | 0.77 | 31 | empty |
| 2 | 55 | 0.51 | 0.86 | 19 | empty |
| 3 | 88 | 0.37 | 0.76 | 22 | empty |
| 4 | 79 | 0.33 | 0.75 | 16 | empty |
| 5 | 50 | 0.29 | 0.75 | 12 | GAL |
Compared structures
- 2VU9 · Crystal structure of botulinum neurotoxin serotype a binding domain in complex with GT1B · 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 2VU9 · PDBe 2VU9 · UniProt P10845
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