Download MendeleyCovalent 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.
4KTX
Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 167-174 stretch
- PDB DOI: https://doi.org/10.2210/pdb4KTX/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Clostridium botulinum A str. Hall, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2013-05-21 Released: 2014-10-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.59 Å
- R-Value Free: 0.298
- R-Value Work: 0.202
- R-Value Observed: 0.207
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Botulinum neurotoxin A light chain | 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 AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peptide inhibitor MPT-DPP-ARG-G-LEU-NH2 | 6 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | E [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | F [auth A], G [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| PGO Query on PGO | D [auth A] | S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N |  | ||
| ZN Query on ZN | C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| 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_001080 Query on PRD_001080 | B | Peptide inhibitor MPT-DPP-ARG-G-LEU-NH2 | Peptide-like / Inhibitor |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.59 Å
- R-Value Free: 0.298
- R-Value Work: 0.202
- R-Value Observed: 0.207
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.41 | α = 90 |
| b = 65.41 | β = 90 |
| c = 200.97 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| REFMAC | refinement |
| DNA | data collection |
| XDS | data reduction |
| XDS | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2014-10-15 Deposition Author(s): Stura, E.A., Vera, L., Guitot, K., Dive, V.
Revision History (Full details and data files)
- Version 1.0: 2014-10-15
Type: Initial release - Version 1.1: 2019-07-17
Changes: Advisory, Data collection, Derived calculations, Refinement description, Source and taxonomy - Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
