8OIG | pdb_00008oig

Crystal Structure of Staphopain C from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb8OIG/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Mutation(s): No

Deposited: 2023-03-22 Released: 2023-06-21
Deposition Author(s): McEwen, A.G., Magoch, M., Napolitano, V., Dubin, G., Wladyka, B.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.116 (Depositor), 0.138 (DCC)
R-Value Work:
0.088 (Depositor), 0.110 (DCC)
R-Value Observed:
0.088 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Staphopain C from Staphylococcus aureus.

Magoch, M., McEwen, A.G., Napolitano, V., Wladyka, B., Dubin, G.

(2023) Molecules 28

PubMed: 37298883 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/molecules28114407
Primary Citation Related Structures:
8OIG

PubMed Abstract:
Staphylococcus aureus is a common opportunistic pathogen of humans and livestock that causes a wide variety of infections. The success of S. aureus as a pathogen depends on the production of an array of virulence factors including cysteine proteases (staphopains)-major secreted proteases of certain strains of the bacterium. Here, we report the three-dimensional structure of staphopain C (ScpA2) of S. aureus , which shows the typical papain-like fold and uncovers a detailed molecular description of the active site. Because the protein is involved in the pathogenesis of a chicken disease, our work provides the foundation for inhibitor design and potential antimicrobial strategies against this pathogen.

Organizational Affiliation

Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.

Macromolecule Content

Total Structure Weight: 59.46 kDa
Atom Count: 4,637
Modeled Residue Count: 519
Deposited Residue Count: 519
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol protease	A, B, C	173	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q8RJP3 (Staphylococcus aureus) Explore Q8RJP3 Go to UniProtKB: Q8RJP3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RJP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	D [auth A], E [auth A], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	F [auth B] G [auth B] H [auth C] I [auth C] J [auth C] F [auth B], G [auth B], H [auth C], I [auth C], J [auth C], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]