1WPX

Crystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase

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	d1wpxa_	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	Serine carboxypeptidase-like	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1wpxb1	All beta proteins	PEBP-like	PEBP-like	Phosphatidylethanolamine binding protein	Carboxypeptidase Y inhibitor	(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	Serine carboxypeptidase-like	8020842	4000709	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta-Hydrolases	8033222	3000102	SCOP2 (2022-06-29)
B	SCOP2 Family	phosphatidylethanolamine binding protein	8020065	4002457	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PEBP-like	8032445	3001269	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_S10	e1wpxA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Peptidase_S10	ECOD (1.6)
B	PBP	e1wpxB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
A	1.10.287.410	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	3.90.280.10	Alpha Beta	Alpha-Beta Complex	Phosphatidylethanolamine-binding Protein	PEBP-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00450	Serine carboxypeptidase (Peptidase_S10)	Serine carboxypeptidase		Domain
B	PF01161	Phosphatidylethanolamine-binding protein (PBP)	Phosphatidylethanolamine-binding protein		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Carboxypeptidase Y	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type carboxypeptidase activity serine-type peptidase activity hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity	catabolic process macroautophagy autophagy cellular process metabolic process process utilizing autophagic mechanism biosynthetic process secondary metabolite biosynthetic process phytochelatin biosynthetic process amide biosynthetic process amide metabolic process phytochelatin metabolic process secondary metabolic process cellular response to stimulus catabolic process macroautophagy autophagy cellular process metabolic process process utilizing autophagic mechanism biosynthetic process secondary metabolite biosynthetic process phytochelatin biosynthetic process amide biosynthetic process amide metabolic process phytochelatin metabolic process secondary metabolic process cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation zymogen activation primary metabolic process gene expression macromolecule biosynthetic process protein maturation proteolysis protein processing protein metabolic process macromolecule metabolic process	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 extracellular region membrane-enclosed lumen vacuolar lumen 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 extracellular region membrane-enclosed lumen vacuolar lumen intracellular organelle lumen organelle lumen fungal-type vacuole lumen endoplasmic reticulum endomembrane system
B	Carboxypeptidase Y inhibitor	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity binding phospholipid binding lipid binding	regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction Ras protein signal transduction regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of Ras protein signal transduction intracellular signaling cassette regulation of cell communication signal transduction	vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane fungal-type vacuole membrane membrane-enclosed lumen vacuolar lumen intracellular organelle lumen organelle lumen fungal-type vacuole lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001563	Peptidase S10, serine carboxypeptidase	Family
A	IPR018202	Serine carboxypeptidase, serine active site	Active Site
A	IPR008442	Propeptide, carboxypeptidase Y	Domain
A	IPR033124	Serine carboxypeptidases, histidine active site	Active Site
A	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
B	IPR036610	PEBP-like superfamily	Homologous Superfamily
B	IPR008914	Phosphatidylethanolamine-binding protein	Family
B	IPR001858	Phosphatidylethanolamine-binding, conserved site	Conserved Site
B	IPR035810	Phosphatidylethanolamine-binding protein, eukaryotic	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : 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

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.