7M6C | pdb_00007m6c

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.233 (Depositor), 0.234 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L8D5Z7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAO (Subject of Investigation/LOI) Query on DAO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.233 (Depositor), 0.234 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Seifert-Davila, W.

Vivas-Ruiz, D.E.

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.