Research workbench
Receptor binding domain of BONT/B in complex with mini-protein binder BOT.2110.4
Analyse Receptor binding domain of BONT/B in complex with mini-protein binder BOT.2110.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VMR
- Type
- protein
- Length
- 915 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; BOT.2110.4
- EC
- 3.4.24.69
- UniProt
- P10844
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 421 | 6% helix, 44% strand | P10844 |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 419 | 6% helix, 44% strand | P10844 |
| C | BOT.2110.4 | protein | 38 | 79% helix, 0% strand | — |
| D | BOT.2110.4 | protein | 37 | 73% helix, 0% strand | — |
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.68 | 0.86 | 37 | empty |
| 2 | 180 | 0.66 | 0.86 | 34 | empty |
| 3 | 76 | 0.60 | 0.89 | 22 | empty |
| 4 | 106 | 0.60 | 0.86 | 23 | empty |
| 5 | 228 | 0.59 | 0.80 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–D · 711 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 697 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 654 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VMR · Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4 · 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 B 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 5VMR · PDBe 5VMR · UniProt P10844
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