1Z8L | pdb_00001z8l

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)
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)
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)
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)
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)
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)
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)
A		e1z8lA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
A		e1z8lA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
A		e1z8lA3	A: HTH	X: HTH	H: winged helix domain	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)
B		e1z8lB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
B		e1z8lB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
B		e1z8lB3	A: HTH	X: HTH	H: winged helix domain	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)
C		e1z8lC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
C		e1z8lC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
C		e1z8lC3	A: HTH	X: HTH	H: winged helix domain	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)
D		e1z8lD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
D		e1z8lD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
D		e1z8lD3	A: HTH	X: HTH	H: winged helix domain	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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		Domain
A, B, C, D	PF02225	PA domain (PA)	PA domain	The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor Swiss:O22925 and members of the RZF family Swiss:O43567. It has been suggested that this domain fo ...	The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor Swiss:O22925 and members of the RZF family Swiss:O43567. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors [1].	Domain

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 binding ion binding oligopeptide binding anion binding Ac-Asp-Glu binding peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity 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	folic acid-containing compound metabolic process modified amino acid metabolic process metabolic process cellular process pteridine-containing compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process system process digestion intestinal absorption digestive system process folic acid-containing compound metabolic process modified amino acid metabolic process metabolic process cellular process pteridine-containing compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process system process digestion intestinal absorption digestive system process intestinal folate absorption positive regulation of cell communication cellular response to stimulus positive regulation of signal transduction regulation of cellular process response to stimulus signaling positive regulation of biological process regulation of signal transduction glutamate receptor signaling pathway cell communication positive regulation of response to stimulus positive regulation of glutamate receptor signaling pathway signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation regulation of glutamate receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 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.