Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a substrate analog peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 16 Sept 2008.
Explore 3DDB in 3D Show helices and sheets RCSB PDB PDBe
3DDB contains 20 α-helices and 25 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 13-14 | 2 | |
| β-strand | 19-23 | 5 | 1 |
| β-strand | 33-39 | 7 | 1 |
| β-strand | 42-48 | 7 | 1 |
| α-helix | 54-56 | 3 | |
| β-strand | 73 | 1 | 2 |
| α-helix | 81-99 | 19 | |
| α-helix | 102-113 | 12 | |
| α-helix | 115-117 | 3 | |
| β-strand | 119 | 1 | 3 |
| β-strand | 126-127 | 2 | 4 |
| β-strand | 128 | 1 | 3 |
| α-helix | 131-133 | 3 | |
| β-strand | 134-138 | 5 | 1 |
| α-helix | 139 | 1 | |
| β-strand | 144-148 | 5 | 1 |
| β-strand | 151-155 | 5 | 1 |
| β-strand | 159 | 1 | 2 |
| β-strand | 164-166 | 3 | 1 |
| β-strand | 184-187 | 4 | 1 |
| β-strand | 192-196 | 5 | 5 |
| α-helix | 200-203 | 4 | |
| β-strand | 213-214 | 2 | 5 |
| α-helix | 215-216 | 2 | |
| α-helix | 217-232 | 16 | |
| α-helix | 236-238 | 3 | |
| β-strand | 242-244 | 3 | 6 |
| α-helix | 249-252 | 4 | |
| β-strand | 257-259 | 3 | 6 |
| α-helix | 260-266 | 7 | |
| α-helix | 270-273 | 4 | |
| α-helix | 276-299 | 24 | |
| β-strand | 302-303 | 2 | 4 |
| α-helix | 310-320 | 11 | |
| β-strand | 324-325 | 2 | 7 |
| β-strand | 331-332 | 2 | 7 |
| α-helix | 335-343 | 9 | |
| α-helix | 344-348 | 5 | |
| α-helix | 351-358 | 8 | |
| β-strand | 372-375 | 4 | 5 |
| β-strand | 385 | 1 | 8 |
| β-strand | 389 | 1 | 8 |
| β-strand | 405 | 1 | 5 |
| α-helix | 410-412 | 3 | |
| β-strand | 414-418 | 5 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Botulinum neurotoxin A light chain | A | protein | 430 | Clostridium botulinum | P0DPI1 (AlphaFold model) |
| Synaptosomal-associated protein 25 | B | protein | 7 | P60880 (AlphaFold model) |
>3DDB_1 Botulinum neurotoxin A light chain (chains A) MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLN PPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGG STIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGY GSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPN RVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKA KSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKV LNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFT GLFEHHHHHH
>3DDB_2 Synaptosomal-associated protein 25 (chains B) RRATKMX
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 1 |
Water and common crystallization additives (SO4) are not listed.
Substrate binding mode and its implication on drug design for botulinum neurotoxin A. Kumaran, D., Rawat, R., Ahmed, S.A. et al. PLoS Pathog (2008) 4:e1000165-e1000165. DOI 10.1371/journal.ppat.1000165 · PubMed
Other PDB entries of the same protein (UniProt P0DPI1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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