2ID4 | pdb_00002id4

The 1.9 A structure of Kex2 in complex with an Ac-R-E-R-K-chloromethyl ketone inhibitor.

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2id4a1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Proprotein convertase P-domain	Kexin, C-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2id4a2	Alpha and beta proteins (a/b)	Subtilisin-like	Subtilisin-like	Subtilases	Kexin, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2id4b1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Proprotein convertase P-domain	Kexin, C-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2id4b2	Alpha and beta proteins (a/b)	Subtilisin-like	Subtilisin-like	Subtilases	Kexin, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	proprotein convertase p-domain	8030317	4003911	SCOP2 (2022-06-29)
A	SCOP2 Family	Subtilases	8030318	4000409	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	galactose-binding domain-like	8042696	3000087	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Subtilisin-like	8042697	3000226	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Subtilisin-like	8042697	3000226	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8042696	3000087	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	P_proprotein	e2id4A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: P_proprotein	ECOD (1.6)
A	Peptidase_S8	e2id4A2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like (From Topology)	T: Subtilisin-like	F: Peptidase_S8	ECOD (1.6)
B	P_proprotein	e2id4B1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: P_proprotein	ECOD (1.6)
B	Peptidase_S8	e2id4B2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like (From Topology)	T: Subtilisin-like	F: Peptidase_S8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.200	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Peptidase S8/S53 domain	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B	3.40.50.200	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Peptidase S8/S53 domain	CATH (4.3.0)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00082	Subtilase family (Peptidase_S8)	Subtilase family	Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7 ...	Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.	Domain
A, B	PF01483	Proprotein convertase P-domain (P_proprotein)	Proprotein convertase P-domain	A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Kexin	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process peptide pheromone maturation	membrane-bounded organelle storage vacuole intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle cellular anatomical structure organelle cytoplasm Golgi apparatus subcompartment Golgi apparatus organelle subcompartment membrane-bounded organelle storage vacuole intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle cellular anatomical structure organelle cytoplasm Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network Golgi membrane membrane bounding membrane of organelle organelle membrane
C, D	Ac-RERK-CMK inhibitor	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023828	Peptidase S8, subtilisin, Ser-active site	Active Site
A, B	IPR022398	Peptidase S8, subtilisin, His-active site	Active Site
A, B	IPR034182	Kexin/furin catalytic domain	Domain
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR002884	P domain	Domain
A, B	IPR000209	Peptidase S8/S53 domain	Domain
A, B	IPR015500	Peptidase S8, subtilisin-related	Family
A, B	IPR036852	Peptidase S8/S53 domain superfamily	Homologous Superfamily
A, B	IPR023827	Peptidase S8, subtilisin, Asp-active site	Active Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
C, D	0QE	RESID: AA0205
C, D	ACE	RESID: AA0205 , AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
C, D	LYK	Parent Component: LYS RESID: AA0205 , AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

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.