7QBD

TC:CD320 in complex with nanobody TC-Nb26

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Six-hairpin glycosidases	8051860	3000970	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051861	3002041	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051861	3002041	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Six-hairpin glycosidases	8051860	3000970	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	Cobalamin_bind	e7qbdA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Cobalamin_bind	ECOD (1.6)
A	DUF4430	e7qbdA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF4430	ECOD (1.6)
B	Cobalamin_bind	e7qbdB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Cobalamin_bind	ECOD (1.6)
B	DUF4430	e7qbdB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF4430	ECOD (1.6)
C	Ldl_recept_a	e7qbdC2	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)
D	Ldl_recept_a	e7qbdD2	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)
E	V-set_12	e7qbdE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E	Heavy Chain	IGHV1	-	transcobalamin-2 \| transcobalamin-2	SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01122	Eukaryotic cobalamin-binding protein (Cobalamin_bind)	Eukaryotic cobalamin-binding protein	-	Repeat
A, B	PF14478	Domain of unknown function (DUF4430) (DUF4430)	Domain of unknown function (DUF4430)	Although this family has overlaps with SLBB, the majority of its sequences are unique. Several family members, eg UniProtKB:A0RGA8, that do not overlap have an LPXTG-cell wall anchor at their C-terminus, a SSF_Family 10_polysaccharide_lyase or Glycos ...	Although this family has overlaps with SLBB, the majority of its sequences are unique. Several family members, eg UniProtKB:A0RGA8, that do not overlap have an LPXTG-cell wall anchor at their C-terminus, a SSF_Family 10_polysaccharide_lyase or Glycosyltransferase structure associated with them in the middle region, as shown by InterPro, as well as this domain at the N-terminus.	Domain
C, D	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Transcobalamin-2	protein binding binding cargo receptor ligand activity vitamin binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization monoatomic ion transmembrane transport inorganic ion transmembrane transport metal ion transport inorganic cation transmembrane transport cobalt ion transport transmembrane transport monoatomic cation transmembrane transport transition metal ion transport localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization monoatomic ion transmembrane transport inorganic ion transmembrane transport metal ion transport inorganic cation transmembrane transport cobalt ion transport transmembrane transport monoatomic cation transmembrane transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular region membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular region membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular space
C, D	CD320 antigen	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity vitamin binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding cargo receptor activity	multicellular organismal process regulation of cellular process regulation of leukocyte activation positive regulation of biological process regulation of cell activation lymphocyte activation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process multicellular organismal process regulation of cellular process regulation of leukocyte activation positive regulation of biological process regulation of cell activation lymphocyte activation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process positive regulation of cellular process regulation of biological process B cell costimulation B cell activation cell activation biological regulation positive regulation of B cell activation immune system process lymphocyte costimulation positive regulation of multicellular organismal process cellular process regulation of lymphocyte activation developmental process multicellular organism development spinal cord development central nervous system development anatomical structure development ventral spinal cord development nervous system development system development localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization positive regulation of cell population proliferation positive regulation of B cell proliferation leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation positive regulation of lymphocyte proliferation B cell proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of small molecule metabolic process small molecule metabolic process metabolic process regulation of vitamin metabolic process regulation of metabolic process vitamin metabolic process	membrane cellular anatomical entity membrane microdomain cell periphery membrane raft plasma membrane raft plasma membrane plasma membrane region caveola membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum membrane cellular anatomical entity membrane microdomain cell periphery membrane raft plasma membrane raft plasma membrane plasma membrane region caveola membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system
E	Antitranscobalamin-nanobody TC-Nb26	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002157	Cobalamin (vitamin B12)-binding protein	Family
A, B	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily
A, B	IPR051588	Eukaryotic Cobalamin Transport	Family
A, B	IPR027954	Transcobalamin-like, C-terminal domain	Domain
C, D	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
C, D	IPR050685	Low-density lipoprotein receptor	Family
C, D	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
C, D	IPR036055	LDL receptor-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P20062	transcobalamin II deficiency megaloblastic anemia Leukoencephalopathies microcystic adenoma adenoma papillary adenoma prostate cancer colorectal cancer esophageal squamous cell carcinoma kidney Wilms tumor follicular thyroid adenoma inborn vitamin B12 deficiency pituitary cancer subependymal giant cell astrocytoma hereditary Wilms tumor transcobalamin II deficiency megaloblastic anemia Leukoencephalopathies microcystic adenoma adenoma papillary adenoma prostate cancer colorectal cancer esophageal squamous cell carcinoma kidney Wilms tumor follicular thyroid adenoma inborn vitamin B12 deficiency pituitary cancer subependymal giant cell astrocytoma hereditary Wilms tumor intellectual disability leukoencephalopathy with vanishing white matter Chagas disease Creutzfeldt Jacob disease inborn errors of metabolism Perlman syndrome autism cleft lip colorectal carcinoma
C, D	Pharos: Q9NPF0	methylmalonic acidemia due to transcobalamin receptor defect heart disease metabolic syndrome X pancreatic intraductal papillary-mucinous neoplasm Hyperammonemia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia large cell medulloblastoma osteosarcoma

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.