2IMA: Botulinum neurotoxin A light-chain

Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by 2,4-dichlorocinnamic hydroxamate. Determined by X-ray diffraction at 1.94 Å resolution. Released 5 Jun 2007.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 7,010
Mol. weight: 102.23 kDa
Ligands: ZN, GB4
Released: 5 Jun 2007

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

Secondary structure: helices and β-sheets

2IMA contains 34 α-helices and 52 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: 16 helices, 26 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
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
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
β-strand	242-243	2	7
β-strand	258-259	2	7
α-helix	260-266	7
α-helix	270-273	4
α-helix	276-299	24
β-strand	302-303	2	4
α-helix	310-321	12
β-strand	324-325	2	8
β-strand	331-332	2	8
α-helix	335-343	9
α-helix	344-348	5
α-helix	351-358	8
β-strand	373-375	3	5
β-strand	385	1	9
β-strand	389	1	9
α-helix	396-398	3
β-strand	405	1	6
α-helix	410-412	3
β-strand	414-416	3	5
α-helix	417	1

Chain B: 18 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	19-23	5	10
α-helix	30-32	3
β-strand	33-39	7	10
β-strand	42-48	7	10
β-strand	73	1	11
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	119	1	12
β-strand	126-127	2	13
β-strand	128	1	12
α-helix	131-133	3
β-strand	134-138	5	10
β-strand	144-148	5	10
β-strand	151-155	5	10
β-strand	159	1	11
β-strand	164-166	3	10
β-strand	184-187	4	10
β-strand	192-194	3	14
β-strand	195-197	3	15
α-helix	206-208	3
β-strand	212-214	3	15
α-helix	217-232	16
α-helix	236-238	3
β-strand	242	1	16
β-strand	259	1	16
α-helix	260-266	7
α-helix	269-272	4
α-helix	276-299	24
β-strand	302-303	2	13
α-helix	310-321	12
β-strand	324-325	2	17
β-strand	331-332	2	17
α-helix	335-343	9
α-helix	344-348	5
α-helix	351-358	8
β-strand	373-375	3	14
β-strand	385	1	18
β-strand	389	1	18
α-helix	402-404	3
β-strand	405	1	15
α-helix	410-412	3
β-strand	414-415	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin A light-chain	A, B	protein	444	Clostridium botulinum	P0DPI0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2IMA_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
GB4	(2E)-3-(2,4-dichlorophenyl)-N-hydroxyacrylamide	C9 H7 Cl2 N O2	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 P0DPI0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RVI 1.6 Å, Structure of the binding domain of BoNT/A mutant H1253K in complex with the GM1a…
6XCF 1.68 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
6XCB 1.74 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
8RVH 1.8 Å, Structure of the binding domain of BoNT/A mutant Y1117V/H1253K in complex with the GD1a…
6XCC 1.9 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
8RVG 1.9 Å, Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a…
6XCD 1.92 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
2ISG 2.0 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form B
2ISH 2.0 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form C
2ISE 2.2 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form A
7KYF 2.33 Å, Botulism Neurooxin Light Chain A app form
6XCE 2.5 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…

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