6DIK

Crystal structure of Bothropstoxin I (BthTX-I) complexed to Chicoric acid

• PDB DOI: https://doi.org/10.2210/pdb6DIK/pdb

• Classification: TOXIN
• Organism(s): Bothrops jararacussu
• Mutation(s): No 


• Deposited: 2018-05-23 Released: 2018-10-03 
• Deposition Author(s): Cardoso, F.F., Salvador, G.H.M., Borges, R.J.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.200 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Structural basis of phospholipase A2-like myotoxin inhibition by chicoric acid, a novel potent inhibitor of ophidian toxins.

Cardoso, F.F., Borges, R.J., Dreyer, T.R., Salvador, G.H.M., Cavalcante, W.L.G., Pai, M.D., Gallacci, M., Fontes, M.R.M.

(2018) Biochim Biophys Acta Gen Subj 1862: 2728-2737

• PubMed: 30251662 
• DOI: https://doi.org/10.1016/j.bbagen.2018.08.002
• Primary Citation of Related Structures:  
  6DIK


• PubMed Abstract: 
  

  Specific compounds found in vegetal species have been demonstrated to be efficient inhibitors of snake toxins, such as phospholipase A ₂ -like (PLA ₂ -like) proteins. These particular proteins, present in several species of vipers (Viperidae), induce a severe local myotoxic effect in prey and human victims, and this effect is often not efficiently neutralized by the regular serum therapy. PLA ₂ -like proteins have been functionally and structurally studied since the early 1990s; however, a comprehensive molecular mechanism was proposed only recently.

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Organizational Affiliation: 

Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: native gel electrophoresis, light scattering

Macromolecule Content

• Total Structure Weight: 28.57 kDa 
• Atom Count: 2,151 
• Modelled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic phospholipase A2 homolog bothropstoxin-1	A, B	121	Bothrops jararacussu	Mutation(s): 0
UniProt
Find proteins for Q90249 (Bothrops jararacussu) Explore Q90249  Go to UniProtKB:  Q90249

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKP	C [auth A]	(2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid C22 H18 O12 YDDGKXBLOXEEMN-IABMMNSOSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BCT	I [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
EOH	J [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.200 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.558	α = 90
b = 71.632	β = 109.02
c = 44.791	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Cardoso, F.F., Salvador, G.H.M., Borges, R.J.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2012/07112-6

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description