4KS6 | pdb_00004ks6

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 166-174 stretch

• PDB DOI: https://doi.org/10.2210/pdb4KS6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Clostridium botulinum A str. Hall, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-17 Released: 2014-06-25 
• Deposition Author(s): Stura, E.A., Vera, L., Guitot, K., Dive, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Covalent modification of the active site cysteine stresses Clostridium botulinum neurotoxin A

Guitot, K., Vera, L., Le Roux, L., Bregant, S., Ptchelkine, D., Beau, F., Stura, E.A., Dive, V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.32 kDa 
• Atom Count: 4,018 
• Modeled Residue Count: 434 
• Deposited Residue Count: 451 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin A light chain	A	445	Clostridium botulinum A str. Hall	Mutation(s): 1  Gene Names: botA, CBO0806, CLC_0862 EC: 3.4.24.69
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore P0DPI1  Go to UniProtKB:  P0DPI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide inhibitor MPT-DPP-DAR-G-DPN-NH2	B	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO	H [auth A], J [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAR	B	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DPN	B	D-PEPTIDE LINKING	C9 H11 N O2		--
DPP	B	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001078	B	Peptide inhibitor MPT-DPP-DAR-G-DPN-NH2	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.634	α = 90
b = 65.634	β = 90
c = 201.725	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Stura, E.A., Vera, L., Guitot, K., Dive, V.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2018-04-25
  Changes: Advisory, Data collection, Source and taxonomy
• Version 1.2: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description