MolNFT v1 · #126042 · protein
Binding domain of botulinum neurotoxin dc in complex with sialylt
5LR0 · Botulinum neurotoxin D/C protein: “Binding domain of botulinum neurotoxin dc in complex with sialylt”. X-ray diffraction, 3 ligands (NGA, GAL, SIA), 8 pockets (best druggability 0.54). MolNFT v1 #126042 on GenesisL1: 3D structure…
- PDB
- 5LR0
- Type
- protein
- Length
- 819 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin D/C protein
- EC
- 3.4.24.69
- UniProt
- A5JGM8
- Ligands
- NGA, GAL, SIA
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin D/C protein (EC 3.4.24.69) | protein | 407 | 8% helix, 49% strand | A5JGM8 |
| B | Botulinum neurotoxin D/C protein (EC 3.4.24.69) | protein | 412 | 9% helix, 49% strand | A5JGM8 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.54 | 0.79 | 37 | empty |
| 2 | 229 | 0.52 | 0.76 | 40 | empty |
| 3 | 127 | 0.49 | 0.79 | 26 | empty |
| 4 | 156 | 0.45 | 0.76 | 24 | empty |
| 5 | 70 | 0.44 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5LR0 · Binding domain of Botulinum Neurotoxin DC in complex with SialylT · 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 A5JGM8
- Elsewhere: RCSB PDB 5LR0 · PDBe 5LR0 · UniProt A5JGM8
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