MolNFT v1 · #149607 · protein
Crystal structure of an engineered botulinum neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1
6G5F: “Crystal structure of an engineered botulinum neurotoxin type B mutant E1191M/S1199Y in complex with human…”. X-ray diffraction, 18 pockets (best druggability 0.85). MolNFT v1 #149607 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6G5F
- Type
- protein
- Length
- 1,303 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Synaptotagmin-1
- EC
- 3.4.24.69
- UniProt
- P10844, P21579
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 440 | 31% helix, 19% strand | P10844 |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 845 | 29% helix, 25% strand | P10844 |
| P | Synaptotagmin-1 | protein | 18 | 83% helix, 0% strand | P21579 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.85 | 0.88 | 90 | GOL, MLI |
| 2 | 340 | 0.75 | 0.86 | 44 | empty |
| 3 | 418 | 0.68 | 0.80 | 44 | empty |
| 4 | 346 | 0.67 | 0.81 | 38 | empty |
| 5 | 182 | 0.66 | 0.86 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5574 Ų buried · 82 hydrogen bonds · protein-protein
- B–P · 736 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6G5F · Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in… · the same entry in another collection · chain A against A, TM-score 1.00
- P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain P against A, TM-score 0.71
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 P10844
- Every structure of UniProt P21579
- Elsewhere: RCSB PDB 6G5F · PDBe 6G5F · UniProt P10844 · UniProt P21579
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