7M6C

Crystal structure of PLA2 from snake venom of peruvian Bothrops atrox

• PDB DOI: https://doi.org/10.2210/pdb7M6C/pdb

• Classification: TOXIN, HYDROLASE
• Organism(s): Bothrops atrox
• Mutation(s): No 


• Deposited: 2021-03-25 Released: 2022-01-12 
• Deposition Author(s): Leonardo, D.A., Chojnowski, G., Simpkin, A., Seifert-Davila, W., Vivas-Ruiz, D.E., Keegan, R., Rigden, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.233 
• R-Value Work: 0.187 

Literature

findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

Chojnowski, G., Simpkin, A., Leonardo, D.A., Seifert-Davila, W., Vivas-Ruiz, D.E., Keegan, R., Rigden, D.

(2022) IUCrJ 9: 86-97

• DOI: https://doi.org/10.1107/S2052252521011088

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.84 kDa 
• Atom Count: 1,080 
• Modelled Residue Count: 122 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic phospholipase A2	A	138	Bothrops atrox	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for A0A1L8D5Z7 (Bothrops atrox) Explore A0A1L8D5Z7  Go to UniProtKB:  A0A1L8D5Z7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAO (Subject of Investigation/LOI)	B [auth A]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.233 
• R-Value Work: 0.187 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.4	α = 90
b = 58.36	β = 90
c = 64.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SIMBAD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Leonardo, D.A., Chojnowski, G., Simpkin, A., Seifert-Davila, W., Vivas-Ruiz, D.E., Keegan, R., Rigden, D.

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description