3CXD

Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	C1-set_4	e3cxdL2	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)
A [auth L]	V-set	e3cxdL1	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)
B [auth H]	C1-set_1	e3cxdH2	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 H]	V-set_12	e3cxdH1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	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 L]	Anti-osteopontin antibody 23C3	L-KAPPA	Mus musculus (house mouse)	IGKV12-4601, IGKJ401, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B [auth H]	Anti-osteopontin antibody 23C3	VH-CH1	Mus musculus (house mouse)	IGHV10-102, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	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 L]	Light Chain	IGKV12	Kappa	a peptide from osteopontin	SAbDab (2024-04-19)
B [auth H]	Heavy Chain	IGHV10	-	a peptide from osteopontin	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth P]	PF00865	Osteopontin (Osteopontin)	Osteopontin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	Fab fragment of anti-osteopontin antibody 23C3, Light chain	-	-	-
B [auth H]	Fab fragment of anti-osteopontin antibody 23C3, Heavy chain	-	-	-
C [auth P]	a peptide from osteopontin	extracellular matrix binding binding ion binding small molecule binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity extracellular matrix binding binding ion binding small molecule binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation positive regulation of cell communication regulation of localization system process positive regulation of steroid hormone secretion regulation of cellular process regulation of system process estradiol secretion developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation positive regulation of cell communication regulation of localization system process positive regulation of steroid hormone secretion regulation of cellular process regulation of system process estradiol secretion cell communication regulation of estradiol secretion localization regulation of steroid hormone secretion regulation of biological quality regulation of biological process regulation of hormone levels organic substance transport lipid transport establishment of localization regulation of secretion endocrine hormone secretion positive regulation of lipid transport lipid export from cell positive regulation of multicellular organismal process regulation of endocrine process regulation of hormone secretion transport signaling steroid hormone secretion positive regulation of biological process regulation of lipid transport positive regulation of secretion by cell organic hydroxy compound transport positive regulation of estradiol secretion hormone secretion secretion by cell positive regulation of hormone secretion regulation of secretion by cell positive regulation of secretion signal release regulation of multicellular organismal process positive regulation of cellular process regulation of signaling secretion regulation of transport biological regulation lipid localization export from cell cell-cell signaling positive regulation of lipid localization endocrine process positive regulation of transport regulation of lipid localization macromolecule localization hormone transport regulation of cell communication positive regulation of signaling multicellular organism development multi-multicellular organism process reproductive process anatomical structure development female pregnancy embryo implantation multi-organism reproductive process cellular response to stimulus response to stimulus cell projection organization developmental growth regulation of cellular response to stress neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation system development regulation of cell projection organization response to external stimulus generation of neurons negative regulation of axonogenesis negative regulation of developmental growth regulation of response to stimulus regulation of collateral sprouting of intact axon in response to injury negative regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting regulation of cellular component organization regulation of developmental process regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis cell development cell growth response to axon injury regulation of response to wounding neurogenesis negative regulation of neurogenesis collateral sprouting of intact axon in response to injury regulation of extent of cell growth axon regeneration regulation of response to stress negative regulation of nervous system development negative regulation of cell differentiation regulation of anatomical structure morphogenesis collateral sprouting regulation of developmental growth developmental cell growth negative regulation of developmental process growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of collateral sprouting of intact axon in response to injury anatomical structure morphogenesis negative regulation of cell development neuron development regulation of growth axonogenesis regulation of cellular component size negative regulation of biological process negative regulation of neuron projection regeneration regulation of cell differentiation regulation of neurogenesis regeneration neuron projection regeneration negative regulation of growth neuron projection morphogenesis response to wounding regulation of axon regeneration negative regulation of cellular component organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration cell morphogenesis cellular component organization regulation of nervous system development cellular response to stress regulation of axonogenesis response to stress negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization regulation of cell size regulation of multicellular organismal development plasma membrane bounded cell projection organization negative regulation of response to stimulus negative regulation of response to wounding negative regulation of neuron projection development regulation of plasma membrane bounded cell projection organization negative regulation of collateral sprouting regulation of anatomical structure size placenta development maternal process involved in female pregnancy multicellular organismal reproductive process animal organ development developmental process involved in reproduction tissue development maternal placenta development decidualization response to organic substance response to lipid response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to organic cyclic compound cellular response to testosterone stimulus response to ketone cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound response to testosterone cellular response to chemical stimulus cellular response to lipid cellular response to organic substance cellular response to ketone response to nutrient levels response to vitamin D response to nutrient response to vitamin cell adhesion positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process homeostatic process regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of bone resorption biomineral tissue development response to cytokine response to macrophage colony-stimulating factor catabolic process lipid catabolic process steroid metabolic process androgen metabolic process hormone metabolic process organic cyclic compound catabolic process steroid catabolic process androgen catabolic process organic substance catabolic process hormone catabolic process lipid metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cytoplasm extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cytoplasm intracellular membrane-bounded organelle endomembrane system membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum perinuclear region of cytoplasm cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth P]	IPR019841	Osteopontin, conserved site	Conserved Site
C [auth P]	IPR002038	Osteopontin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth P]	Pharos: P10451	malignant glioma breast carcinoma kidney disease Mammary Neoplasms, Experimental cirrhosis of liver adenocarcinoma allergic contact dermatitis heart disease calcinosis pulmonary fibrosis mixed glioma allergic disease pneumonia granular cell carcinoma breast cancer malignant glioma breast carcinoma kidney disease Mammary Neoplasms, Experimental cirrhosis of liver adenocarcinoma allergic contact dermatitis heart disease calcinosis pulmonary fibrosis mixed glioma allergic disease pneumonia granular cell carcinoma breast cancer proteinuria heart valve disease tubular adenocarcinoma uremia alcoholic liver diseases asbestosis focal segmental glomerulosclerosis psoriasis cribriform carcinoma of breast acute kidney failure nasopharyngeal carcinoma Down syndrome invasive ductal breast carcinoma adrenal cortex carcinoma osteoporosis Duchenne muscular dystrophy limb-girdle muscular dystrophy esophageal adenocarcinoma lung adenocarcinoma atrial fibrillation pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma pleural neoplasm gout lytic metastatic bone lesion malignant pancreatic neoplasm tuberculosis congestive heart failure ulcerative colitis idiopathic interstitial pneumonia cutaneous lupus erythematosus interstitial cystitis nephrolithiasis drug-induced liver injury ovarian cancer ductal breast carcinoma in situ pancreatic ductal adenocarcinoma lung benign neoplasm Becker muscular dystrophy pilocytic astrocytoma glioblastoma brain cancer malignant ependymoma cancer sarcoidosis mesothelioma cribriform carcinoma injury myopathy intracerebral hemorrhage non-small cell lung carcinoma leukoencephalopathy with vanishing white matter pancreas disease endometriosis pancreatic intraductal papillary-mucinous carcinoma lung cancer benign mesothelioma pleural cancer glioma pneumonitis

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.