3BKY

Crystal Structure of Chimeric Antibody C2H7 Fab in complex with a CD20 Peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
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 [auth H]	d3bkyh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth H]	d3bkyh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	V-set_8	e3bkyH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A [auth H]	C1-set_1	e3bkyH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth L]	C1-set_4	e3bkyL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e3bkyL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth H]	C2H7	VH-CH1	Chimeric (chimeric)	IGHV1-1201, IGHJ103, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B [auth L]	C2H7	L-KAPPA	Chimeric (chimeric)	IGKV4-7201, IGKJ501, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV1	-	b-lymphocyte antigen cd20	SAbDab (2024-04-19)
B [auth L]	Light Chain	IGKV4	Kappa	b-lymphocyte antigen cd20	SAbDab (2024-04-19)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth H]	Zuberitamab	MS4A1/CD20	Therapeutic SAbDab (2024-04-19)
B [auth L]	Zuberitamab	MS4A1/CD20	Therapeutic SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth P]	PF04103	CD20-like family (CD20)	CD20-like family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	the Fab fragment of chimeric 2H7, heavy chain	-	-	-
B [auth L]	the Fab fragment of chimeric 2H7, light chain	-	-	-
C [auth P]	B-lymphocyte antigen CD20	protein-containing complex binding binding immunoglobulin binding epidermal growth factor receptor binding protein binding signaling receptor binding growth factor receptor binding MHC protein complex binding MHC class II protein complex binding identical protein binding	multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation immune system process mononuclear cell proliferation lymphocyte proliferation cellular process localization transport multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation immune system process mononuclear cell proliferation lymphocyte proliferation cellular process localization transport monoatomic ion transport calcium ion import into cytosol monoatomic cation transport establishment of localization calcium ion transport metal ion transport store-operated calcium entry developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response humoral immune response regulation of calcium ion transport regulation of localization positive regulation of cation transmembrane transport positive regulation of calcium ion transport positive regulation of calcium ion import positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport regulation of calcium ion import regulation of monoatomic ion transport import across plasma membrane inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport regulation of transmembrane transport calcium ion import across plasma membrane regulation of calcium ion import across plasma membrane import into cell monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport positive regulation of calcium ion import across plasma membrane positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport regulation of metal ion transport positive regulation of cellular process calcium ion transmembrane import into cytosol regulation of transport inorganic cation import across plasma membrane positive regulation of transport inorganic ion import across plasma membrane regulation of monoatomic cation transmembrane transport calcium ion import calcium ion transmembrane transport cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen membrane microdomain membrane raft plasma membrane raft plasma membrane region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth P]	IPR030417	Membrane-spanning 4-domains subfamily A	Family
C [auth P]	IPR007237	CD20-like family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth P]	Pharos: P11836	common variable immunodeficiency non-small cell lung carcinoma lung adenocarcinoma immunodeficiency, common variable, 5 B-cell chronic lymphocytic leukemia squamous cell carcinoma malignant colon neoplasm Microscopic polyarteritis nodosa ovarian cyst pemphigus vulgaris atypical teratoid rhabdoid tumor breast cancer sinusitis corpus luteum cyst systemic sclerosis common variable immunodeficiency non-small cell lung carcinoma lung adenocarcinoma immunodeficiency, common variable, 5 B-cell chronic lymphocytic leukemia squamous cell carcinoma malignant colon neoplasm Microscopic polyarteritis nodosa ovarian cyst pemphigus vulgaris atypical teratoid rhabdoid tumor breast cancer sinusitis corpus luteum cyst systemic sclerosis invasive ductal breast carcinoma lung cancer malignant glioma nasopharyngeal carcinoma osteosarcoma periodontitis B cell deficiency rheumatoid arthritis cutaneous lupus erythematosus Sjogren syndrome glioblastoma thrombotic thrombocytopenic purpura large cell medulloblastoma lung carcinoma ovarian cancer pemphigus foliaceus agammaglobulinemia primary progressive multiple sclerosis secondary progressive multiple sclerosis ductal breast carcinoma in situ granulomatosis with polyangiitis ulcerative colitis interstitial cystitis

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.