MolNFT v1 · #149612 · protein
Crystal structure of the binding domain of botulinum neurotoxin type B in complex with human synaptotagmin 1
6G5K: “Crystal structure of the binding domain of botulinum neurotoxin type B in complex with human synaptotagmin 1”. X-ray diffraction, 8 pockets (best druggability 0.67). MolNFT v1 #149612 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6G5K
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- 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
- 8 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 421 | 6% helix, 45% strand | P10844 |
| C | Synaptotagmin-1 | protein | 16 | 81% helix, 0% strand | P21579 |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 424 | 6% helix, 45% strand | P10844 |
| D | Synaptotagmin-1 | protein | 15 | 87% helix, 0% strand | P21579 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.67 | 0.81 | 48 | empty |
| 2 | 84 | 0.65 | 0.91 | 22 | empty |
| 3 | 103 | 0.62 | 0.87 | 24 | empty |
| 4 | 93 | 0.61 | 0.88 | 21 | empty |
| 5 | 549 | 0.61 | 0.74 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–C · 709 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 664 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 409 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6G5K · Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with… · the same entry in another collection · chain C against C, 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 0.97
- P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain D against A, TM-score 0.56
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 6G5K · PDBe 6G5K · UniProt P10844 · UniProt P21579
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