3DS9: Botulinum neurotoxin type A

A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate. Determined by X-ray diffraction at 1.76 Å resolution. Released 30 Sept 2008.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 3,523
Mol. weight: 49.03 kDa
Ligands: ZN, NI
Released: 30 Sept 2008

Explore 3DS9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DS9 contains 18 α-helices and 23 β-strands across 2 chains. 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.

Chain A: 17 helices, 23 β-strands

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	61-62	2
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	119	1	2
β-strand	126-127	2	3
β-strand	128	1	2
α-helix	131-133	3
β-strand	134-138	5	1
β-strand	144-148	5	1
β-strand	151-155	5	1
β-strand	164-166	3	1
β-strand	184-187	4	1
β-strand	192-196	5	4
β-strand	213-214	2	4
α-helix	215-216	2
α-helix	217-232	16
β-strand	242-244	3	5
β-strand	257-259	3	5
α-helix	260-266	7
α-helix	268-273	6
α-helix	276-299	24
β-strand	302-303	2	3
α-helix	310-321	12
β-strand	324-325	2	6
β-strand	331-332	2	6
α-helix	335-343	9
α-helix	344-348	5
α-helix	351-358	8
β-strand	372-375	4	4
β-strand	385	1	7
β-strand	389	1	7
α-helix	402-404	3
β-strand	405	1	4
α-helix	410-412	3
β-strand	414-415	2	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	199-202	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type A	A	protein	417	Clostridium botulinum	P0DPI1 (AlphaFold model)
octapeptide I1 inhibitor	B	protein	8

Sequence of entity 1 (A), FASTA

>3DS9_1 Botulinum neurotoxin type A (chains A)
MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLN
PPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGG
STIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGY
GSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPN
RVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKA
KSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKV
LNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK

Sequence of entity 2 (B), FASTA

>3DS9_2 octapeptide I1 inhibitor (chains B)
XRWTAMLG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NI	Nickel (II) ion	Ni	1

Primary citation

A Potent Peptidomimetic Inhibitor of Botulinum Neurotoxin Serotype A Has a Very Different Conformation than SNAP-25 Substrate. Zuniga, J.E., Schmidt, J.J., Fenn, T. et al. Structure (2008) 16:1588-1597. DOI 10.1016/j.str.2008.07.011 · PubMed

Other PDB entries of the same protein (UniProt P0DPI1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BON 1.2 Å, Structure of the C. botulinum neurotoxin serotype A with Zn2+ cofactor bound
4EL4 1.2 Å, Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S…
3BOK 1.25 Å, Structure of the C. botulinum neurotoxin serotype A apo-enzyme
3BOO 1.4 Å, Structure of the C. botulinum neurotoxin serotype A with an inhibitory peptide bound
5MK6 1.45 Å, Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal…
3C8B 1.47 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
3DDA 1.5 Å, Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a…
3QW7 1.5 Å, Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a…
3C8A 1.52 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
3C89 1.58 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
2VU9 1.6 Å, Crystal structure of botulinum neurotoxin serotype a binding domain in complex with GT1B
3C88 1.6 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…

Browse structure collections

About this viewer

MolViewer shows 3DS9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.