Research workbench
Receptor binding domain of botulinum neurotoxin a in complex with rat SV2C
Analyse Receptor binding domain of botulinum neurotoxin a in complex with rat SV2C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JMC
- Type
- protein
- Length
- 2,039 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type a; Synaptic vesicle glycoprotein 2C
- EC
- 3.4.24.69
- UniProt
- P10845, Q9Z2I6
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 420 | 6% helix, 45% strand | P10845 |
| B | Synaptic vesicle glycoprotein 2C | protein | 91 | 3% helix, 54% strand | Q9Z2I6 |
| C | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 417 | 7% helix, 46% strand | P10845 |
| D, F | Synaptic vesicle glycoprotein 2C | protein | 92 | 3% helix, 61% strand | Q9Z2I6 |
| E | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 419 | 6% helix, 47% strand | P10845 |
| G | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 419 | 8% helix, 46% strand | P10845 |
| H | Synaptic vesicle glycoprotein 2C | protein | 89 | 3% helix, 60% strand | Q9Z2I6 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.73 | 0.80 | 42 | empty |
| 2 | 602 | 0.70 | 0.79 | 46 | empty |
| 3 | 338 | 0.67 | 0.81 | 39 | empty |
| 4 | 383 | 0.67 | 0.80 | 50 | empty |
| 5 | 412 | 0.66 | 0.79 | 49 | empty |
Interfaces
10 interfaces between chains.
- A–B · 670 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 646 Ų buried · 13 hydrogen bonds · protein-protein
- B–G · 624 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 618 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5JMC · Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Z2I6 · AlphaFold monomer V2.0 prediction for synaptic vesicle glycoprotein 2C (Q9Z2I6) · 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 P10845
- Every structure of UniProt Q9Z2I6
- Elsewhere: RCSB PDB 5JMC · PDBe 5JMC · UniProt P10845 · UniProt Q9Z2I6
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