6RLO

Crystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6rlob2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6rlob1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth D]	d6rlod2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth D]	d6rlod1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d6rlof2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d6rlof1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K [auth H]	d6rloh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K [auth H]	d6rloh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6rloa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth C]	d6rloc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth E]	d6rloe_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J [auth G]	d6rlog_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	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)
B	C1-set_4	e6rloB2	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	V-set	e6rloB1	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)
E [auth D]	C1-set_4	e6rloD1	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)
E [auth D]	V-set	e6rloD2	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)
H [auth F]	C1-set_4	e6rloF1	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)
H [auth F]	V-set	e6rloF2	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)
K [auth H]	C1-set_4	e6rloH1	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)
K [auth H]	V-set	e6rloH2	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 I]	CD81_like_LEL	e6rloI1	A: few secondary structure elements	X: Tetraspanin extracellular domain (From Topology)	H: Tetraspanin extracellular domain (From Topology)	T: Tetraspanin extracellular domain	F: CD81_like_LEL	ECOD (1.6)
F [auth J]	CD81_like_LEL	e6rloJ1	A: few secondary structure elements	X: Tetraspanin extracellular domain (From Topology)	H: Tetraspanin extracellular domain (From Topology)	T: Tetraspanin extracellular domain	F: CD81_like_LEL	ECOD (1.6)
I [auth K]	CD81_like_LEL	e6rloK1	A: few secondary structure elements	X: Tetraspanin extracellular domain (From Topology)	H: Tetraspanin extracellular domain (From Topology)	T: Tetraspanin extracellular domain	F: CD81_like_LEL	ECOD (1.6)
L	CD81_like_LEL	e6rloL1	A: few secondary structure elements	X: Tetraspanin extracellular domain (From Topology)	H: Tetraspanin extracellular domain (From Topology)	T: Tetraspanin extracellular domain	F: CD81_like_LEL	ECOD (1.6)
A	C1-set_1	e6rloA2	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)
A	V-set_12	e6rloA1	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)
D [auth C]	C1-set_1	e6rloC1	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 C]	V-set_12	e6rloC2	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)
G [auth E]	C1-set_1	e6rloE2	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)
G [auth E]	V-set_12	e6rloE1	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)
J [auth G]	C1-set_1	e6rloG1	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)
J [auth G]	V-set_12	e6rloG2	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
B, E [auth D], H [auth F], K [auth H]	Light Chain	IGKV4	Kappa	cd9 antigen	SAbDab (2024-11-15)
A, D [auth C], G [auth E], J [auth G]	Heavy Chain	IGHV3	-	cd9 antigen	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth I], F [auth J], I [auth K], L	PF00335	Tetraspanin family (Tetraspanin)	Tetraspanin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E [auth D], H [auth F], K [auth H]	AT1412dm Fab Fragment (Light Chain)	-	-	-
C [auth I], F [auth J], I [auth K], L	CD9 antigen	cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding	sperm-egg recognition sexual reproduction cell-cell recognition reproductive process fertilization cell recognition cellular process single fertilization developmental process tissue regeneration skeletal muscle tissue regeneration cellular developmental process developmental growth myoblast fusion sperm-egg recognition sexual reproduction cell-cell recognition reproductive process fertilization cell recognition cellular process single fertilization developmental process tissue regeneration skeletal muscle tissue regeneration cellular developmental process developmental growth myoblast fusion growth cell-cell fusion myotube differentiation involved in skeletal muscle regeneration muscle cell differentiation regeneration myotube differentiation muscle structure development syncytium formation by plasma membrane fusion anatomical structure morphogenesis cell differentiation myoblast fusion involved in skeletal muscle regeneration anatomical structure development anatomical structure formation involved in morphogenesis striated muscle cell differentiation syncytium formation localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cell population proliferation multicellular organismal process regulation of body fluid levels regulation of cellular process response to stimulus negative regulation of biological process regulation of cell activation negative regulation of cell adhesion negative regulation of platelet activation regulation of coagulation regulation of biological quality response to wounding regulation of biological process negative regulation of homotypic cell-cell adhesion negative regulation of wound healing negative regulation of blood coagulation response to external stimulus blood coagulation negative regulation of hemostasis regulation of platelet activation regulation of response to stimulus negative regulation of response to external stimulus negative regulation of cell-cell adhesion regulation of wound healing negative regulation of multicellular organismal process platelet activation regulation of response to external stimulus homotypic cell-cell adhesion regulation of response to wounding cell adhesion cell-cell adhesion response to stress regulation of response to stress negative regulation of cellular process coagulation regulation of cell-cell adhesion regulation of multicellular organismal process regulation of hemostasis wound healing negative regulation of response to stimulus regulation of homotypic cell-cell adhesion regulation of cell adhesion regulation of blood coagulation biological regulation hemostasis cell activation negative regulation of platelet aggregation negative regulation of response to wounding platelet aggregation negative regulation of cell activation regulation of platelet aggregation negative regulation of coagulation regulation of cell motility regulation of leukocyte migration macrophage migration leukocyte migration regulation of macrophage migration immune system process regulation of locomotion mononuclear cell migration regulation of cell migration myeloid leukocyte migration cell migration regulation of immune system process regulation of mononuclear cell migration cell motility locomotion membrane organization membrane fusion plasma membrane fusion multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism cellular component organization fusion of sperm to egg plasma membrane involved in single fertilization plasma membrane organization cellular component organization or biogenesis endomembrane system organization negative regulation of cell population proliferation regulation of cell population proliferation cellular response to stimulus cellular response to low-density lipoprotein particle stimulus response to endogenous stimulus response to chemical response to lipoprotein particle response to nitrogen compound cellular response to lipoprotein particle stimulus glial cell migration nervous system development neurogenesis multicellular organism development gliogenesis system development cellular component assembly involved in morphogenesis myelin assembly cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly cell junction assembly axon ensheathment ensheathment of neurons cell-cell junction assembly cell-cell junction organization myelination cell junction organization paranodal junction assembly	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle protein-containing complex platelet alpha granule membrane endomembrane system secretory granule secretory vesicle platelet alpha granule secretory granule membrane
A, D [auth C], G [auth E], J [auth G]	AT1412dm Fab Fragment (Heavy Chain)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth I], F [auth J], I [auth K], L	IPR042055	CD9, extracellular domain	Domain
C [auth I], F [auth J], I [auth K], L	IPR008952	Tetraspanin, EC2 domain superfamily	Homologous Superfamily
C [auth I], F [auth J], I [auth K], L	IPR000301	Tetraspanin, animals	Family
C [auth I], F [auth J], I [auth K], L	IPR018503	Tetraspanin, conserved site	Conserved Site
C [auth I], F [auth J], I [auth K], L	IPR018499	Tetraspanin/Peripherin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth I], F [auth J], I [auth K], L	Pharos: P21926	glioblastoma acute myeloid leukemia colorectal cancer giant cell glioblastoma Nerve Degeneration non-small cell lung carcinoma germ cell tumor cirrhosis of liver embryonal neoplasm prostate cancer facioscapulohumeral muscular dystrophy tuberculosis invasive ductal breast carcinoma limb-girdle muscular dystrophy ankylosing spondylitis glioblastoma acute myeloid leukemia colorectal cancer giant cell glioblastoma Nerve Degeneration non-small cell lung carcinoma germ cell tumor cirrhosis of liver embryonal neoplasm prostate cancer facioscapulohumeral muscular dystrophy tuberculosis invasive ductal breast carcinoma limb-girdle muscular dystrophy ankylosing spondylitis malignant glioma medulloblastoma colorectal adenoma ovarian cancer Duchenne muscular dystrophy primary biliary cholangitis Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung cancer Becker muscular dystrophy malignant mesothelioma dermatomyositis pancreatic ductal adenocarcinoma ductal breast carcinoma in situ progressive supranuclear palsy esophageal adenocarcinoma psoriasis gastric carcinoma interstitial cystitis large cell medulloblastoma malignant ependymoma cancer malignant pancreatic neoplasm colorectal carcinoma osteosarcoma Down syndrome pilocytic astrocytoma