1DKI

CRYSTAL STRUCTURE OF THE ZYMOGEN FORM OF STREPTOCOCCAL PYROGENIC EXOTOXIN B ACTIVE SITE (C47S) MUTANT

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
D	d1dkid_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Streptococcal pyrogenic exotoxin B	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
A	d1dkia_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Streptococcal pyrogenic exotoxin B	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
B	d1dkib_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Streptococcal pyrogenic exotoxin B	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
C	d1dkic_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Streptococcal pyrogenic exotoxin B	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cysteine proteinases	8034056	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8034056	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8034056	3001808	SCOP2B (2022-06-29)
C	SCOP2 Family	Papain-like	8021676	4000859	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Cysteine proteinases	8034056	3001808	SCOP2 (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	Peptidase_C10	e1dkiA3	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C10	ECOD (1.6)
B	Peptidase_C10	e1dkiB2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C10	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.70.50	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	3.30.910.30	Alpha Beta	2-Layer Sandwich	Protein Binding, DinI Protein	Chain A	CATH (4.3.0)
A	3.90.70.50	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.30.910.30	Alpha Beta	2-Layer Sandwich	Protein Binding, DinI Protein	Chain A	CATH (4.3.0)
B	3.90.70.50	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.30.910.30	Alpha Beta	2-Layer Sandwich	Protein Binding, DinI Protein	Chain A	CATH (4.3.0)
C	3.90.70.50	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.30.910.30	Alpha Beta	2-Layer Sandwich	Protein Binding, DinI Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13734	Spi protease inhibitor (Inhibitor_I69)	Spi protease inhibitor	-	Family
A, B, C, D	PF01640	Peptidase C10 family (Peptidase_C10)	Peptidase C10 family	This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate. The catalytic residues of histidine and cy ...	This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate. The catalytic residues of histidine and cysteine are brought close together at the active site by the folding of the active peptide.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	PYROGENIC EXOTOXIN B ZYMOGEN	toxin activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated response to host defenses response to external stimulus biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated perturbation of host process response to host immune response symbiont-mediated evasion of host immune response response to host symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated response to host defenses response to external stimulus biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated perturbation of host process response to host immune response symbiont-mediated evasion of host immune response response to host response to external biotic stimulus modulation of process of another organism defense response defense response to symbiont cell death symbiont-induced defense-related programmed cell death defense response to other organism response to stress cellular process programmed cell death proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host autophagy symbiont-mediated perturbation of host autophagy	cellular anatomical structure extracellular region host extracellular space host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region host cell cytosol host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000200	Peptidase C10, streptopain	Family
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR025896	Spi protease inhibitor	Domain
A, B, C, D	IPR044934	Peptidase C10, streptopain superfmaily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	streptopain M-CSA #598	Cysteine protease which is a virulance factor for many infectious diseases. It displays structural homology with papains despite having such low sequence identity with the superfamily that it merits being placed in a completely separate class.	Defined by 3 residues: SER:A-165 [auth A-47]HIS:A-313 [auth A-195]TRP:A-330 [auth A-212] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.22.10 (UniProt) Search M-CSA Motif + EC 3.4.22.10

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.