5CBA

3B4 in complex with CXCL13 - 3B4-CXCL13

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d5cbaa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5cbac_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5cbab1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5cbab2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5cbad1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5cbad2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5cbae_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5cbaf_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	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)
F	SCOP2B Superfamily	Interleukin 8-like chemokines	8061449	3001955	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	V-set_8	e5cbaA1	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)
C	V-set_8	e5cbaC1	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)
B	V-set_3	e5cbaB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D	V-set_3	e5cbaD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
E	IL8_1	e5cbaE1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8_1	ECOD (1.6)
F	IL8_1	e5cbaF1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
F	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Heavy Chain	IGHV1	-	c-x-c motif chemokine 13	SAbDab (2024-04-19)
B, D	Light Chain	IGLV2	Lambda	c-x-c motif chemokine 13	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B, D	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
E, F	PF00048	Small cytokines (intecrine/chemokine), interleukin-8 like (IL8)	Small cytokines (intecrine/chemokine), interleukin-8 like	Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	3b4 heavy chain	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex extracellular region
B, D	3b4 light chain	binding antigen binding	response to stimulus immune response immune system process adaptive immune response	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex
E, F	C-X-C motif chemokine 13	binding molecular function activator activity signaling receptor binding G protein-coupled receptor binding signaling receptor activator activity protein binding cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding receptor ligand activity CCR10 chemokine receptor binding binding molecular function activator activity signaling receptor binding G protein-coupled receptor binding signaling receptor activator activity protein binding cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding receptor ligand activity CCR10 chemokine receptor binding CCR chemokine receptor binding CXCR chemokine receptor binding CXCR3 chemokine receptor binding fibroblast growth factor binding growth factor binding CXCR5 chemokine receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis regulation of angiogenesis anatomical structure development anatomical structure formation involved in morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development positive regulation of cytosolic calcium ion concentration regulation of biological quality chronic inflammatory response response to stimulus defense response response to stress inflammatory response cellular response to stimulus negative regulation of locomotion regulation of cell motility regulation of cellular process endothelial cell migration negative regulation of biological process negative regulation of chemotaxis negative regulation of endothelial cell migration endothelial cell chemotaxis to fibroblast growth factor tissue migration taxis negative regulation of epithelial cell migration negative regulation of cell chemotaxis to fibroblast growth factor cell migration negative regulation of cell migration chemotaxis regulation of cellular response to growth factor stimulus response to external stimulus negative regulation of endothelial cell chemotaxis to fibroblast growth factor epithelium migration regulation of response to stimulus response to chemical regulation of locomotion negative regulation of response to external stimulus negative regulation of cell motility negative regulation of endothelial cell chemotaxis negative regulation of multicellular organismal process cellular response to fibroblast growth factor stimulus response to fibroblast growth factor cellular response to growth factor stimulus regulation of response to external stimulus negative regulation of cellular response to growth factor stimulus cellular response to endogenous stimulus ameboidal-type cell migration regulation of cell migration negative regulation of cellular process regulation of endothelial cell migration epithelial cell migration endothelial cell chemotaxis regulation of cell chemotaxis to fibroblast growth factor cell motility locomotion regulation of epithelial cell migration cell chemotaxis regulation of endothelial cell chemotaxis to fibroblast growth factor regulation of endothelial cell chemotaxis negative regulation of response to stimulus response to endogenous stimulus regulation of chemotaxis cellular response to chemical stimulus cell chemotaxis to fibroblast growth factor cellular process response to growth factor immune response immune system process cell-cell adhesion mediated by integrin positive regulation of cell adhesion mediated by integrin positive regulation of cell adhesion regulation of cell adhesion regulation of cell adhesion mediated by integrin positive regulation of biological process regulation of cell-cell adhesion mediated by integrin positive regulation of cell-cell adhesion positive regulation of cell-cell adhesion mediated by integrin cell adhesion cell-cell adhesion cell adhesion mediated by integrin regulation of cell-cell adhesion positive regulation of cellular process neutrophil chemotaxis neutrophil migration granulocyte migration leukocyte migration granulocyte chemotaxis myeloid leukocyte migration leukocyte chemotaxis response to organic substance cell surface receptor signaling pathway signaling response to cytokine response to chemokine cytokine-mediated signaling pathway cellular response to chemokine chemokine-mediated signaling pathway cell communication G protein-coupled receptor signaling pathway cellular response to cytokine stimulus signal transduction cellular response to organic substance cell-cell signaling biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of humoral immune response humoral immune response regulation of immune response regulation of immune system process lymphocyte chemotaxis lymphocyte migration mononuclear cell migration B cell chemotaxis lymphocyte chemotaxis across high endothelial venule defense response to bacterium defense response to other organism regulation of cellular component organization positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly regulation of integrin activation protein-containing complex assembly cellular component organization or biogenesis integrin activation positive regulation of integrin activation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains germinal center formation adaptive immune response defense response to symbiont antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide positive regulation of locomotion positive regulation of T cell chemotaxis positive regulation of chemotaxis positive regulation of cell migration regulation of lymphocyte chemotaxis regulation of mononuclear cell migration positive regulation of immune system process regulation of leukocyte chemotaxis positive regulation of lymphocyte migration regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of T cell migration regulation of T cell chemotaxis regulation of lymphocyte migration positive regulation of lymphocyte chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility positive regulation of mononuclear cell migration T cell chemotaxis positive regulation of T cell migration positive regulation of leukocyte migration T cell migration activation of GTPase activity positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity	extracellular region cellular anatomical entity extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C	IPR013106	Immunoglobulin V-set domain	Domain
A, C	IPR007110	Immunoglobulin-like domain	Domain
B, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D	IPR003599	Immunoglobulin subtype	Domain
B, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D	IPR013106	Immunoglobulin V-set domain	Domain
B, D	IPR007110	Immunoglobulin-like domain	Domain
E, F	IPR001811	Chemokine interleukin-8-like domain	Domain
E, F	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
E, F	IPR001089	CXC chemokine	Family
E, F	IPR039809	Chemokine beta/gamma/delta	Family
E, F	IPR033899	CXC Chemokine domain	Domain
E, F	IPR018048	CXC chemokine, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: O43927	Liver Cirrhosis, Experimental malignant mesothelioma Sjogren syndrome autoimmune disease chronic obstructive pulmonary disease endometriosis juvenile dermatomyositis malignant glioma ovarian cancer ulcerative colitis breast cancer cutaneous lupus erythematosus head and neck cancer periodontitis sinusitis Liver Cirrhosis, Experimental malignant mesothelioma Sjogren syndrome autoimmune disease chronic obstructive pulmonary disease endometriosis juvenile dermatomyositis malignant glioma ovarian cancer ulcerative colitis breast cancer cutaneous lupus erythematosus head and neck cancer periodontitis sinusitis breast carcinoma ductal breast carcinoma in situ interstitial cystitis lung adenocarcinoma non-small cell lung carcinoma psoriasis

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.