5TZT

Crystal structure of human CD47 ECD bound to Fab of C47B161

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d5tztb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d5tztl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d5tzta_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth H]	d5tzth_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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 B]	C1-set_4	e5tztB1	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 B]	V-set	e5tztB2	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)
C [auth L]	C1-set_4	e5tztL2	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)
C [auth L]	V-set	e5tztL1	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 A]	V-set_8	e5tztA2	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 [auth A]	C1-set_1	e5tztA1	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)
D [auth H]	V-set_8	e5tztH2	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)
D [auth H]	C1-set_1	e5tztH1	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)
E [auth C]	V-set_CD47	e5tztC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_CD47	ECOD (1.6)
F [auth D]	V-set_CD47	e5tztD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_CD47	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	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 B], C [auth L]	Fab C47B161	L-KAPPA	Homo sapiens (human)	IGKV1-11701, IGKJ201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202449-0)
B [auth A], D [auth H]	Fab C47B161	VH-CH1	Homo sapiens (human)	IGHV1-301, IGHJ101, IGHJ601, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202449-0)
E [auth C], F [auth D]	CD47	1V-LIKE	Homo sapiens (human)	CD47	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202449-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth B], C [auth L]	Light Chain	IGKV1	Kappa	leukocyte surface antigen cd47	SAbDab (2024-12-13)
B [auth A], D [auth H]	Heavy Chain	IGHV1	-	leukocyte surface antigen cd47	SAbDab (2024-12-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], F [auth D]	PF08204	CD47 immunoglobulin-like domain (V-set_CD47)	CD47 immunoglobulin-like domain	This family represents the CD47 leukocyte antigen V-set like Ig domain [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], C [auth L]	Light Chain of Fab C47B161	-	-	-
B [auth A], D [auth H]	Heavy Chain of Fab C47B161	-	-	-
E [auth C], F [auth D]	Leukocyte surface antigen CD47	molecular transducer activity signaling receptor activity thrombospondin receptor activity cell adhesion molecule binding protein binding binding cell adhesion mediator activity cell-cell adhesion mediator activity protein-containing complex binding fibrinogen binding protein binding involved in heterotypic cell-cell adhesion	positive regulation of locomotion regulation of cell motility regulation of cellular process positive regulation of monocyte extravasation positive regulation of biological process positive regulation of cell migration monocyte extravasation positive regulation of cell motility cellular extravasation myeloid leukocyte migration regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process positive regulation of locomotion regulation of cell motility regulation of cellular process positive regulation of monocyte extravasation positive regulation of biological process positive regulation of cell migration monocyte extravasation positive regulation of cell motility cellular extravasation myeloid leukocyte migration regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration positive regulation of immune system process locomotion positive regulation of cellular process regulation of biological process regulation of leukocyte migration biological regulation positive regulation of leukocyte migration leukocyte migration immune system process regulation of locomotion mononuclear cell migration regulation of monocyte extravasation cellular process regulation of cellular extravasation positive regulation of cellular extravasation regulation of defense response response to stimulus regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development apoptotic process cell death programmed cell death cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway signaling cell communication signal transduction regulation of biosynthetic process regulation of type II interferon production type II interferon production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process cytokine production regulation of cytokine production metabolic process regulation of macromolecule biosynthetic process regulation of multicellular organismal process macromolecule metabolic process regulation of metabolic process positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis regulation of tumor necrosis factor production tumor necrosis factor superfamily cytokine production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production interleukin-10 production regulation of interleukin-10 production regulation of nitric oxide biosynthetic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process regulation of nitric oxide metabolic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation biological process involved in interspecies interaction between organisms immune response response to other organism response to type II interferon response to cytokine defense response to symbiont cellular response to type II interferon response to biotic stimulus response to peptide response to chemical defense response to other organism innate immune response cellular response to cytokine stimulus response to external biotic stimulus negative regulation of biological process negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis negative regulation of cellular process negative regulation of cellular component organization immune response-regulating cell surface receptor signaling pathway regulation of signal transduction regulation of Fc receptor mediated stimulatory signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of signaling immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of cell communication regulation of immune response activation of immune response interleukin-6 production regulation of interleukin-6 production regulation of interleukin-12 production interleukin-12 production response to interleukin-12 cellular response to interleukin-12 cellular response to interleukin-1 response to interleukin-1 regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation T cell activation positive regulation of leukocyte activation positive regulation of T cell activation cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly cellular component biogenesis cellular component assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization ATP transport nitrogen compound transport organic anion transport nucleotide transport purine ribonucleotide transport carbohydrate derivative transport purine nucleotide transport adenine nucleotide transport ATP export nucleobase-containing compound transport organophosphate ester transport	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule membrane specific granule extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C], F [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth C], F [auth D]	IPR013270	CD47 immunoglobulin-like	Domain
E [auth C], F [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth C], F [auth D]	IPR037805	Leukocyte surface antigen CD47, IgV	Domain
E [auth C], F [auth D]	IPR007110	Immunoglobulin-like domain	Domain
E [auth C], F [auth D]	IPR006704	Leukocyte surface antigen CD47	Family
E [auth C], F [auth D]	IPR013147	CD47-like, transmembrane	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth C], F [auth D]	Pharos: Q08722	malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor primitive neuroectodermal tumor bipolar disorder Tourette syndrome cystic fibrosis Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung cancer malignant glioma medulloblastoma osteosarcoma malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor primitive neuroectodermal tumor bipolar disorder Tourette syndrome cystic fibrosis Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease atopic eczema psoriasis breast cancer ulcerative colitis dermatomyositis glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma atypical teratoid rhabdoid tumor Sjogren syndrome cancer Duchenne muscular dystrophy invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth A], D [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420
E [auth C], F [auth D]	PCA	Parent Component: GLN RESID: AA0031 , AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.