1X9Y | pdb_00001x9y

The prostaphopain B structure

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1x9ya1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Staphopain SspB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1x9ya2	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Staphopain B, prodomain	Staphopain B, prodomain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1x9ya3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d1x9yc1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Staphopain SspB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d1x9yc2	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Staphopain B, prodomain	Staphopain B, prodomain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d1x9yc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d1x9yd1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Staphopain SspB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d1x9yd2	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Staphopain B, prodomain	Staphopain B, prodomain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d1x9yd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1x9yb1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Staphopain SspB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1x9yb2	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Staphopain B, prodomain	Staphopain B, prodomain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1x9yb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Staphopain B, prodomain	8031350	4003676	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cystatin/monellin	8043728	3000441	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8034081	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cystatin/monellin	8043728	3000441	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8034081	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cystatin/monellin	8043728	3000441	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8034081	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8034081	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cystatin/monellin	8043728	3000441	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Staphopain_pro	e1x9yA1	A: a+b two layers	X: Cystatin-like	H: Cystatin/monellin	T: Cystatin/monellin	F: Staphopain_pro	ECOD (v294.1)
A	Peptidase_C2	e1x9yA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Peptidase_C2	ECOD (v294.1)
C	Glyco_hydro_18	e1x9yC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Glyco_hydro_18	ECOD (v294.1)
C	Peptidase_C2	e1x9yC2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Peptidase_C2	ECOD (v294.1)
D	Glyco_hydro_18	e1x9yD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Glyco_hydro_18	ECOD (v294.1)
D	Peptidase_C2	e1x9yD2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Peptidase_C2	ECOD (v294.1)
B	Glyco_hydro_18	e1x9yB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Glyco_hydro_18	ECOD (v294.1)
B	Peptidase_C2	e1x9yB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Peptidase_C2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.500.10	Alpha Beta	Roll	prostaphopain b, domain 1	Staphopain proregion domain	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.10.500.10	Alpha Beta	Roll	prostaphopain b, domain 1	Staphopain proregion domain	CATH (4.3.0)
C	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	3.10.500.10	Alpha Beta	Roll	prostaphopain b, domain 1	Staphopain proregion domain	CATH (4.3.0)
D	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.10.500.10	Alpha Beta	Roll	prostaphopain b, domain 1	Staphopain proregion domain	CATH (4.3.0)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	cysteine proteinase	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR028076	Staphopain proregion	Domain
A, B, C, D	IPR025660	Cysteine peptidase, histidine active site	Active Site
A, B, C, D	IPR037155	Staphopain proregion superfamily	Homologous Superfamily
A, B, C, D	IPR008750	Staphopain peptidase C47	Family
A, B, C, D	IPR046350	Cystatin superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	staphopain M-CSA #805	Staphopain B is a possible virulence factor from Staphylococcus aureus, and is a member of the papain superfamily of cysteine proteases. It is able to degrade elastin, fibrogen, fibronectin and kininogen. Exhibits a strong preference for substrates where arginine is preceded by a hydrophobic amino acid. Promotes detachment of primary human keratinocytes. Along with other extracellular proteases is involved in colonization and infection of human tissues Staphostatin B is a specific inhibitor of staphopain B encoded in the same operon. Inhibition of staphopains is a target for treatment of antibiotic-resistant S. aureus infections. It is a produced as an inactive proenzyme, which is comprised of the active part of the enzyme, the mature form, and a covalently bonded inhibitory pro-region. Activation of the enzyme requires cleavage of the N terminal inhibitory pro-region (staphostatin B)	Defined by 4 residues: GLN:A-203 [auth A-237]CYS:A-209 [auth A-243]HIS:A-306 [auth A-340]ASN:A-326 [auth A-360] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.22 (PDB Primary Data) Search M-CSA Motif + EC 3.4.22

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.