4WTB

BthTX-I, a svPLA2s-like toxin, complexed with zinc ions

PDB DOI: https://doi.org/10.2210/pdb4WTB/pdb

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

Deposited: 2014-10-29 Released: 2015-11-11
Deposition Author(s): Borges, R.J., Fontes, M.R.M.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP), CAPES

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.234
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Functional and structural studies of a Phospholipase A2-like protein complexed to zinc ions: Insights on its myotoxicity and inhibition mechanism.

Borges, R.J., Cardoso, F.F., Fernandes, C.A., Dreyer, T.R., de Moraes, D.S., Floriano, R.S., Rodrigues-Simioni, L., Fontes, M.R.

(2017) Biochim Biophys Acta 1861: 3199-3209

PubMed: 27531710 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2016.08.003
Primary Citation of Related Structures:
4WTB

PubMed Abstract:
One of the main challenges in snakebite envenomation treatment is the development of stable, versatile and efficient anti-venom therapies. Local myotoxicity in accidents involving snakes from the Bothrops genus is still a consequence of serum therapy inefficient neutralization that may lead to permanent sequelae in their victims. One of the classes of toxins that participate in muscle necrosis is the PLA ₂-like proteins. The aim of this work was to investigate the role of zinc ions in the inhibition of PLA ₂-like proteins and to advance the current knowledge of their action mechanism.

Organizational Affiliation

Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rua Prof. Dr. Antonio Celso Wagner Zanin, s/n, 18618-689 Botucatu, SP, Brazil.

Macromolecule Content

Total Structure Weight: 27.93 kDa
Atom Count: 2,023
Modelled Residue Count: 242
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q90249
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	C [auth A], D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B]	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.234
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.58	α = 90
b = 56.58	β = 90
c = 129.53	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-11

Deposition Author(s):

Borges, R.J.

Fontes, M.R.M.

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	12/06502-5
Sao Paulo Research Foundation (FAPESP)	Brazil	09/12155-3
CAPES	Brazil	1592/2011

Revision History (Full details and data files)

Version 1.0: 2015-11-11
Type: Initial release
Version 1.1: 2017-05-17
Changes: Database references
Version 1.2: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description