4KS6

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.252
R-Value Work: 0.193
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DPI1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A]	E [auth A], F [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A]
PGO Query on PGO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A]	H [auth A], J [auth A]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain J [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPP Query on 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 Query on PRD_001078	B	Peptide inhibitor MPT-DPP-DAR-G-DPN-NH2	Peptide-like / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.252
R-Value Work: 0.193
R-Value Observed: 0.196
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

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Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

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Deposit Data

Help and Resources

4KS6

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2