4ZJX | pdb_00004zjx

Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with a Novel Cyclic Peptide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ZJX/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Clostridium botulinum, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-29 Released: 2016-06-01 
• Deposition Author(s): Kumaran, D., Swaminathan, S.
• Funding Organization(s): Defense Threat Reduction Agency (DTRA)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with a Novel Cyclic Peptide Inhibitor

Kumaran, D., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 51.05 kDa 
• Atom Count: 3,640 
• Modeled Residue Count: 426 
• Deposited Residue Count: 441 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin type A	A	432	Clostridium botulinum	Mutation(s): 0  Gene Names: botA, atx, bna 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
circular peptide inhibitor	B	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB	B	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002231	B	circular peptide inhibitor	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.889	α = 90
b = 66.367	β = 98.51
c = 64.863	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Kumaran, D., Swaminathan, S.

---

Funding Organization	Location	Grant Number
Defense Threat Reduction Agency (DTRA)	United States	--

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Advisory, Author supporting evidence, Derived calculations
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary