2IMC: Botulinum neurotoxin A light-chain

Clostridium botulinum Neurotoxin Serotype A Light Chain, Residues 1-424. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 Jun 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 6,934
Mol. weight: 101.77 kDa
Ligands: ZN
Released: 5 Jun 2007

Explore 2IMC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IMC contains 37 α-helices and 50 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: 20 helices, 24 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	54-56	3
α-helix	60-63	4
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	192-194	3	5
β-strand	195-198	4	6
β-strand	211-214	4	6
α-helix	217-232	16
α-helix	236-238	3
α-helix	260-266	7
α-helix	268-272	5
α-helix	276-298	23
β-strand	302-303	2	4
α-helix	310-321	12
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
α-helix	368-370	3
β-strand	373-375	3	5
β-strand	385	1	8
β-strand	389	1	8
α-helix	399-404	6
β-strand	405	1	6
α-helix	410-412	3
β-strand	414-417	4	5

Chain B: 17 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	9
α-helix	30-32	3
β-strand	33-39	7	9
β-strand	42-48	7	9
β-strand	73	1	10
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	119	1	11
β-strand	126-127	2	12
β-strand	128	1	11
α-helix	131-133	3
β-strand	134-138	5	9
α-helix	139	1
β-strand	144-148	5	9
β-strand	151-155	5	9
β-strand	159	1	10
β-strand	164-166	3	9
β-strand	184-187	4	9
β-strand	192-194	3	13
β-strand	195-197	3	14
β-strand	212-214	3	14
α-helix	217-232	16
α-helix	236-238	3
β-strand	242	1	15
β-strand	259	1	15
α-helix	260-266	7
α-helix	268-273	6
α-helix	276-298	23
β-strand	302-303	2	12
α-helix	310-321	12
β-strand	324-325	2	16
β-strand	331-332	2	16
α-helix	335-343	9
α-helix	344-348	5
α-helix	351-358	8
β-strand	373-375	3	13
β-strand	385	1	17
β-strand	389	1	17
α-helix	402-404	3
β-strand	405	1	14
α-helix	410-412	3
β-strand	414-415	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin A light-chain	A, B	protein	444	Clostridium botulinum	P0DPI1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2IMC_1 Botulinum neurotoxin A light-chain (chains A, B)
MGSSHHHHHHSSGLVPRGSHMQFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHN
KIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYS
TDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADI
IQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVT
LAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQEN
EFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDK
LYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAAN
FNGQNTEINNMNFTKLKNFTGLFE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain Complexed with Small-Molecule Inhibitors Highlight Active-Site Flexibility. Silvaggi, N.R., Boldt, G.E., Hixon, M.S. et al. Chem Biol (2007) 14:533-542. DOI 10.1016/j.chembiol.2007.03.014 · 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…

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