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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Botulinum neurotoxin A light chain
A
445Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)Mutation(s): 1 
Gene Names: botA (bna)
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Go to UniProtKB:  P0DPI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide inhibitor MPT-DPP-DAR-G-DPN-NH2
B
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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Download CCD File 
A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001078
Query on PRD_001078
BPeptide inhibitor MPT-DPP-DAR-G-DPN-NH2Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.634α = 90.00
b = 65.634β = 90.00
c = 201.725γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
REFMACphasing
XDSdata scaling
XDSdata reduction
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Advisory, Data collection, Source and taxonomy