1Z8L

Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1z8lb1	All alpha proteins	N-cbl like	Transferrin receptor-like dimerisation domain	Transferrin receptor-like dimerisation domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1z8lb2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	PA domain	PA domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1z8lb3	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	FolH catalytic domain-like	Glutamate carboxypeptidase II FOLH1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1z8la1	All alpha proteins	N-cbl like	Transferrin receptor-like dimerisation domain	Transferrin receptor-like dimerisation domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1z8la2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	PA domain	PA domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1z8la3	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	FolH catalytic domain-like	Glutamate carboxypeptidase II FOLH1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1z8lc1	All alpha proteins	N-cbl like	Transferrin receptor-like dimerisation domain	Transferrin receptor-like dimerisation domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1z8lc2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	PA domain	PA domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1z8lc3	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	FolH catalytic domain-like	Glutamate carboxypeptidase II FOLH1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1z8ld1	All alpha proteins	N-cbl like	Transferrin receptor-like dimerisation domain	Transferrin receptor-like dimerisation domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1z8ld2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	PA domain	PA domain	Glutamate carboxypeptidase II	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1z8ld3	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	FolH catalytic domain-like	Glutamate carboxypeptidase II FOLH1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PA domain	8039260	3000955	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Transferrin receptor-like dimerisation domain	8039258	3000375	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transferrin receptor-like dimerisation domain	8039258	3000375	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PA domain	8039260	3000955	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Transferrin receptor-like dimerisation domain	8039258	3000375	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PA domain	8039260	3000955	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Transferrin receptor-like dimerisation domain	8039258	3000375	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zn-dependent exopeptidases	8039261	3000662	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PA domain	8039260	3000955	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	PF04253	e1z8lB1	A: alpha bundles	X: N-cbl like	H: Transferrin receptor ectodomain, C-terminal domain (From Topology)	T: Transferrin receptor ectodomain, C-terminal domain	F: PF04253	ECOD (1.6)
B	PF04389	e1z8lB2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: PF04389	ECOD (1.6)
B	PF02225	e1z8lB3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF02225	ECOD (1.6)
A	PF04253	e1z8lA1	A: alpha bundles	X: N-cbl like	H: Transferrin receptor ectodomain, C-terminal domain (From Topology)	T: Transferrin receptor ectodomain, C-terminal domain	F: PF04253	ECOD (1.6)
A	PF04389	e1z8lA2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: PF04389	ECOD (1.6)
A	PF02225	e1z8lA3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF02225	ECOD (1.6)
C	PF04253	e1z8lC1	A: alpha bundles	X: N-cbl like	H: Transferrin receptor ectodomain, C-terminal domain (From Topology)	T: Transferrin receptor ectodomain, C-terminal domain	F: PF04253	ECOD (1.6)
C	PF04389	e1z8lC2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: PF04389	ECOD (1.6)
C	PF02225	e1z8lC3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF02225	ECOD (1.6)
D	PF04253	e1z8lD1	A: alpha bundles	X: N-cbl like	H: Transferrin receptor ectodomain, C-terminal domain (From Topology)	T: Transferrin receptor ectodomain, C-terminal domain	F: PF04253	ECOD (1.6)
D	PF04389	e1z8lD2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: PF04389	ECOD (1.6)
D	PF02225	e1z8lD3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF02225	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
B	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
B	1.20.930.40	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)
A	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
A	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
A	1.20.930.40	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)
C	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
C	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
C	1.20.930.40	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)
D	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
D	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
D	1.20.930.40	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04253	Transferrin receptor-like dimerisation domain (TFR_dimer)	Transferrin receptor-like dimerisation domain	This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.	Domain
A, B, C, D	PF04389	Peptidase family M28 (Peptidase_M28)	Peptidase family M28	-	Family
A, B, C, D	PF02225	PA domain (PA)	PA domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glutamate carboxypeptidase II	peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity amide binding binding ion binding oligopeptide binding anion binding peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity amide binding binding ion binding oligopeptide binding anion binding Ac-Asp-Glu binding small molecule binding tetrahydrofolyl-poly(glutamate) polymer binding dipeptidase activity cation binding metal ion binding	C-terminal protein amino acid modification organonitrogen compound metabolic process primary metabolic process protein deglutamylation organic substance metabolic process peptidyl-glutamic acid modification C-terminal protein deglutamylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification C-terminal protein amino acid modification organonitrogen compound metabolic process primary metabolic process protein deglutamylation organic substance metabolic process peptidyl-glutamic acid modification C-terminal protein deglutamylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification organic cyclic compound metabolic process folic acid-containing compound metabolic process cellular metabolic process cellular process pteridine-containing compound metabolic process cellular modified amino acid metabolic process proteolysis	membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell surface cell periphery plasma membrane membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell surface cell periphery plasma membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007484	Peptidase M28	Domain
A, B, C, D	IPR036757	Transferrin receptor-like, dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR039373	Transferrin receptor protein 1/Glutamate carboxypeptidase 2-like	Family
A, B, C, D	IPR046450	PA domain superfamily	Homologous Superfamily
A, B, C, D	IPR007365	Transferrin receptor-like, dimerisation domain	Domain
A, B, C, D	IPR003137	PA domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q04609	prostate cancer schizophrenia adrenal cortex carcinoma carcinoma Down syndrome medulloblastoma oligodendroglioma Positron emission tomography subependymal giant cell astrocytoma astrocytic tumor colorectal cancer large cell medulloblastoma Pick disease progressive supranuclear palsy psoriasis prostate cancer schizophrenia adrenal cortex carcinoma carcinoma Down syndrome medulloblastoma oligodendroglioma Positron emission tomography subependymal giant cell astrocytoma astrocytic tumor colorectal cancer large cell medulloblastoma Pick disease progressive supranuclear palsy psoriasis ulcerative colitis breast cancer depressive disorder malignant ependymoma non-small cell lung carcinoma pilocytic astrocytoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.