7KYF: Botulism Neurooxin Light Chain A app form

Name: PDB 7KYF: Botulism Neurooxin Light Chain A app form
Published: 2021-04-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Botulism Neurooxin Light Chain A app form. Determined by X-ray diffraction at 2.33 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Clostridium botulinum
Chains: 1
Atoms: 3,275
Mol. weight: 48.3 kDa
Ligands: ZN, XC1
Released: 14 Apr 2021

Explore 7KYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KYF contains 16 α-helices and 22 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.

Chain C: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
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
α-helix	139	1
β-strand	144-148	5	1
β-strand	151-155	5	1
β-strand	164	1	1
β-strand	184-187	4	1
β-strand	192-196	5	4
β-strand	213-214	2	4
α-helix	217-232	16
α-helix	236-238	3
β-strand	242	1	5
β-strand	259	1	5
α-helix	260-266	7
α-helix	270-272	3
α-helix	276-283	8
α-helix	285-298	14
β-strand	302-303	2	3
α-helix	310-320	11
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
β-strand	414-415	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bont/A1	C	protein	417	Clostridium botulinum	P0DPI0 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7KYF_1 Bont/A1 (chains C)
MPFVNKQFNYKDPVNGVDIAYIKIPNVGVMQPVKAFKIHNKIWVIPERDTFTNPEEGDLN
PPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGG
STIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGY
GSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPN
RVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKA
KSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKV
LNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
XC1	N-[(3,5-dichlorophenyl)sulfonyl]-L-isoleucyl-N-hydroxy-L-norvalinamide	C17 H25 Cl2 N3 O5 S	1

Primary citation

Discovery of Dipeptides as Potent Botulinum Neurotoxin A Light-Chain Inhibitors. Amezcua, M., Cruz, R.S., Ku, A. et al. ACS Med Chem Lett (2021) 12:295-301. DOI 10.1021/acsmedchemlett.0c00674 · 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…
2IMA 1.94 Å, Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by…
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
6XCE 2.5 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…

Browse structure collections

About this viewer

MolViewer shows 7KYF 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.