3BI1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of methotrexate-Glu

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	d3bi1a1	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	d3bi1a2	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	d3bi1a3	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	SCOP2 Family	Transferrin receptor-like dimerisation domain	8026879	4000989	SCOP2 (2022-06-29)
A	SCOP2 Family	PA domain	8026881	4003501	SCOP2 (2022-06-29)
A	SCOP2 Family	FolH catalytic domain-like	8026882	4000590	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Transferrin receptor-like dimerisation domain	8039258	3000375	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PA domain	8039260	3000955	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-dependent exopeptidases	8039261	3000662	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	TFR_dimer	e3bi1A1	A: alpha bundles	X: N-cbl like	H: Transferrin receptor ectodomain, C-terminal domain (From Topology)	T: Transferrin receptor ectodomain, C-terminal domain	F: TFR_dimer	ECOD (1.6)
A	Peptidase_M28	e3bi1A2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M28	ECOD (1.6)
A	PA	e3bi1A3	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: PA	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	PF04389	Peptidase family M28 (Peptidase_M28)	Peptidase family M28	-	Family
A	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	Glutamate carboxypeptidase 2	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 primary metabolic process protein deglutamylation peptidyl-glutamic acid modification C-terminal protein deglutamylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification folic acid-containing compound metabolic process C-terminal protein amino acid modification primary metabolic process protein deglutamylation peptidyl-glutamic acid modification C-terminal protein deglutamylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification folic acid-containing compound metabolic process modified amino acid metabolic process pteridine-containing compound metabolic process proteolysis	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	IPR007484	Peptidase M28	Domain
A	IPR036757	Transferrin receptor-like, dimerisation domain superfamily	Homologous Superfamily
A	IPR039373	Transferrin receptor protein 1/Glutamate carboxypeptidase 2-like	Family
A	IPR046450	PA domain superfamily	Homologous Superfamily
A	IPR007365	Transferrin receptor-like, dimerisation domain	Domain
A	IPR003137	PA domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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.