Research workbench
Crystal structure of clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (INH1)
Analyse Crystal structure of clostridium botulinum neurotoxin serotype F catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FIE
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type F; Fragment of vesicle-associated membrane protein 2
- EC
- 3.4.24.69
- UniProt
- Q57236, P63027
- Ligands
- ZN, NH2
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type F (EC 3.4.24.69) | protein | 407 | 35% helix, 19% strand | Q57236 |
| B | Botulinum neurotoxin type F (EC 3.4.24.69) | protein | 402 | 32% helix, 20% strand | Q57236 |
| C, D | Fragment of vesicle-associated membrane protein 2 | protein | 34 | 12% helix, 9% strand | P63027 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.80 | 0.84 | 70 | empty |
| 2 | 214 | 0.63 | 0.83 | 28 | empty |
| 3 | 253 | 0.62 | 0.81 | 26 | empty |
| 4 | 132 | 0.50 | 0.80 | 28 | empty |
| 5 | 85 | 0.49 | 0.83 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2008 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1909 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 255 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 93 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 d-amino (D-amino acid).
Compared structures
- 3FIE · Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an… · the same entry in another collection · chain C against C, TM-score 1.00
- P63027 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63027) · a predicted model of the same protein · chain C against A, TM-score 0.24
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 Q57236
- Every structure of UniProt P63027
- Elsewhere: RCSB PDB 3FIE · PDBe 3FIE · UniProt Q57236 · UniProt P63027
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