5V8R: Small Molecule Inhibitor ABS-143

Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 6,939
Mol. weight: 102.27 kDa
Ligands: ZN, 90J
Released: 26 Jul 2017

Explore 5V8R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V8R contains 36 α-helices and 49 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	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	192-198	7	4
α-helix	209-210	2
β-strand	211-214	4	4
α-helix	217-232	16
β-strand	242	1	5
β-strand	259	1	5
α-helix	260-266	7
α-helix	268-273	6
α-helix	276-298	23
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	396-398	3
α-helix	402-404	3
β-strand	405	1	4
α-helix	410-412	3
β-strand	414-415	2	4

Chain B: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	19-23	5	8
α-helix	30-32	3
β-strand	33-39	7	8
β-strand	42-48	7	8
β-strand	73	1	9
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	119	1	10
β-strand	126-127	2	11
β-strand	128	1	10
α-helix	131-133	3
β-strand	134-138	5	8
α-helix	139	1
β-strand	144-148	5	8
β-strand	151-155	5	8
β-strand	159	1	9
β-strand	164-166	3	8
β-strand	184-187	4	8
β-strand	192-194	3	12
β-strand	195-197	3	13
α-helix	206-208	3
β-strand	212-214	3	13
α-helix	217-232	16
α-helix	236-238	3
β-strand	242	1	14
β-strand	259	1	14
α-helix	260-266	7
α-helix	268-272	5
α-helix	276-299	24
β-strand	302-303	2	11
α-helix	310-321	12
β-strand	324-325	2	15
β-strand	331-332	2	15
α-helix	335-343	9
α-helix	344-348	5
α-helix	351-358	8
β-strand	373-375	3	12
β-strand	385	1	16
β-strand	389	1	16
α-helix	402-404	3
β-strand	405	1	13
α-helix	410-412	3
β-strand	414-415	2	12

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>5V8R_1 Botulinum neurotoxin type A (chains A, B)
MGSSHHHHHHSSGLVPRGSHMQFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHN
KIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYS
TDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADI
IQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVT
LAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQEN
EFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDK
LYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAAN
FNGQNTEINNMNFTKLKNFTGLFE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
90J	N-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]-2-sulfanylacetamide	C11 H10 F N3 O S	2

Primary citation

Small molecule metalloprotease inhibitor with in vitro, ex vivo and in vivo efficacy against botulinum neurotoxin serotype A. Jacobson, A.R., Adler, M., Silvaggi, N.R. et al. Toxicon (2017) 137:36-47. DOI 10.1016/j.toxicon.2017.06.016 · 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

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