MolNFT v1 · #137235 · protein
Receptor binding domain of BONT/B in complex with mini-protein binder BOT.0671.2
5VID · Botulinum neurotoxin type B: “Receptor binding domain of BONT/B in complex with mini-protein binder BOT.0671.2”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #137235 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VID
- Type
- protein
- Length
- 2,233 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; BOT.0671.2
- EC
- 3.4.24.69
- UniProt
- P10844
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 420 | 5% helix, 44% strand | P10844 |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 412 | 6% helix, 45% strand | P10844 |
| C | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 426 | 6% helix, 45% strand | P10844 |
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 415 | 6% helix, 46% strand | P10844 |
| E | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 405 | 6% helix, 46% strand | P10844 |
| F | BOT.0671.2 | protein | 40 | 75% helix, 0% strand | — |
| G, I | BOT.0671.2 | protein | 39 | 79% helix, 0% strand | — |
| H | BOT.0671.2 | protein | 37 | 76% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.83 | 0.88 | 69 | empty |
| 2 | 546 | 0.80 | 0.86 | 71 | empty |
| 3 | 231 | 0.73 | 0.88 | 31 | empty |
| 4 | 185 | 0.70 | 0.88 | 33 | empty |
| 5 | 566 | 0.67 | 0.77 | 49 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1665 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 1007 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 685 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 679 Ų buried · 8 hydrogen bonds · protein-protein
- C–I · 650 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5VID · Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 · the same entry in another collection · chain I against I, 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
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
- Elsewhere: RCSB PDB 5VID · PDBe 5VID · UniProt P10844
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