4S2R | pdb_00004s2r

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth Q]	SCOP2 Family	Peptidase M24 C-terminal domain-like	8045050	4004278	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Family	Cytosolic X-prolyl aminopeptidase domain 2-like	8045059	4004281	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Family	Creatinase/prolidase N-terminal domain	8054217	4000535	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Family	Creatinase/aminopeptidase-like	8054219	4000207	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Superfamily	Peptidase M24 C-terminal domain-like	8054215	3002284	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Superfamily	Creatinase/prolidase N-terminal domain-like	8054216	3000538	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Superfamily	Creatinase/prolidase N-terminal domain-like	8054218	3000538	SCOP2 (2022-06-29)
B [auth Q]	SCOP2 Superfamily	Creatinase/aminopeptidase catalytic domain-like	8054220	3000126	SCOP2 (2022-06-29)
A [auth P]	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8054220	3000126	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8054218	3000538	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Peptidase M24 C-terminal domain-like	8054215	3002284	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8054216	3000538	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)
B [auth Q]	PNKP_ligase	e4s2rQ1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: PNKP_ligase	ECOD (v294.1)
A [auth P]	PNKP_ligase	e4s2rP1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: PNKP_ligase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth Q]	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
B [auth Q]	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
A [auth P]	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
A [auth P]	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth P], B [auth Q]	PF00557	Metallopeptidase family M24 (Peptidase_M24)	Metallopeptidase family M24	This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3].	Domain
A [auth P], B [auth Q]	PF16189	Creatinase/Prolidase N-terminal domain (Creatinase_N_2)	Creatinase/Prolidase N-terminal domain		Domain
A [auth P], B [auth Q]	PF16188	C-terminal region of peptidase_M24 (Peptidase_M24_C)	C-terminal region of peptidase_M24	This is a short region at the C-terminus of a number of metallo-peptidases of the M24 family.	Domain
A [auth P], B [auth Q]	PF01321	Creatinase/Prolidase N-terminal domain (Creatinase_N)	Creatinase/Prolidase N-terminal domain	This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], B [auth Q]	Protein APP-1	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth P], B [auth Q]	IPR000587	Creatinase, N-terminal	Domain
A [auth P], B [auth Q]	IPR050422	Xaa-Pro aminopeptidase P	Family
A [auth P], B [auth Q]	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal	Homologous Superfamily
A [auth P], B [auth Q]	IPR033740	Aminopeptidase P	Domain
A [auth P], B [auth Q]	IPR032416	Peptidase M24, C-terminal domain	Domain
A [auth P], B [auth Q]	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
A [auth P], B [auth Q]	IPR000994	Peptidase M24	Domain

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.