4XZU

Crystal Structure of the Human Factor VIII C2 Domain in Complex with Murine 3E6 Inhibitory Antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4xzua_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth E]	d4xzue_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4xzub2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4xzub1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth F]	d4xzuf2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth F]	d4xzuf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth M]	d4xzum_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth G]	d4xzug_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)	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)
C [auth M]	SCOP2B Superfamily	galactose-binding domain-like	8041137	3000087	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	galactose-binding domain-like	8041137	3000087	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	PF07654	e4xzuA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF07686	e4xzuA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth E]	PF07654	e4xzuE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth E]	PF07686	e4xzuE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF07654	e4xzuB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07686	e4xzuB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth F]	PF07654	e4xzuF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth F]	PF07686	e4xzuF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth M]	PF00754	e4xzuM1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	ECOD (1.6)
F [auth G]	PF00754	e4xzuG1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	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)
D [auth E]	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)
E [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth M]	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
F [auth G]	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	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, D [auth E]	3E6 Fab	VH-CH1	Mus musculus (house mouse)	IGHV9-2-101, IGHJ201, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)
B, E [auth F]	3E6 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV4-5501, IGKJ101, IGKJ201, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth E]	Heavy Chain	IGHV9	-	coagulation factor viii	SAbDab (2024-04-26)
B, E [auth F]	Light Chain	IGKV4	Kappa	coagulation factor viii	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth M], F [auth G]	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth E]	3E6 antibody Fab heavy chain	-	-	-
B, E [auth F]	3E6 antibody Fab light chain	-	-	-
C [auth M], F [auth G]	Coagulation factor VIII	oxidoreductase activity catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding acute-phase response defense response inflammatory response multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding acute-phase response defense response inflammatory response acute inflammatory response cellular biosynthetic process protein maturation organic substance metabolic process blood coagulation, intrinsic pathway blood coagulation, fibrin clot formation organic substance biosynthetic process protein metabolic process protein activation cascade organonitrogen compound metabolic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle cytoplasm endoplasmic reticulum lumen membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region membrane bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule vesicle platelet alpha granule lumen cell periphery plasma membrane COPII-coated ER to Golgi transport vesicle coated vesicle extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth M], F [auth G]	IPR033138	Multicopper oxidases, conserved site	Conserved Site
C [auth M], F [auth G]	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
C [auth M], F [auth G]	IPR011707	Multicopper oxidase-like, N-terminal	Domain
C [auth M], F [auth G]	IPR024715	Coagulation factor 5/8-like	Family
C [auth M], F [auth G]	IPR008972	Cupredoxin	Homologous Superfamily
C [auth M], F [auth G]	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
C [auth M], F [auth G]	IPR011706	Multicopper oxidase, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth M], F [auth G]	Pharos: P00451	hemophilia A thrombophilia Venous Thrombosis autoimmune disease lung carcinoma MALT lymphoma nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor acquired hemophilia thrombotic disease astrocytic tumor ductal breast carcinoma in situ hemophilia hereditary von Willebrand disease hemophilia A thrombophilia Venous Thrombosis autoimmune disease lung carcinoma MALT lymphoma nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor acquired hemophilia thrombotic disease astrocytic tumor ductal breast carcinoma in situ hemophilia hereditary von Willebrand disease lung adenocarcinoma malignant ependymoma medulloblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm severe hemophilia A acquired von willebrand syndrome tuberculosis atypical teratoid rhabdoid tumor congenital factor XI deficiency invasive ductal breast carcinoma lung cancer malignant pancreatic neoplasm mild hemophilia A pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia arthropathy vascular disease hemophilia B large cell medulloblastoma

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.