3BN9 | pdb_00003bn9

Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2

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 [auth B]	d3bn9b_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Matriptase MTSP1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d3bn9a_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Matriptase MTSP1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3bn9c2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3bn9c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3bn9e2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3bn9e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d3bn9d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Camelid IG heavy chain variable domain, VHh	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d3bn9d2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3bn9f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Camelid IG heavy chain variable domain, VHh	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3bn9f2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	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)
A [auth B]	SCOP2B Superfamily	Trypsin-like serine proteases	8035635	3000114	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Trypsin-like serine proteases	8035635	3000114	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091519	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091519	3000071	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 [auth B]	Lipocalin	e3bn9B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
D [auth A]	Lipocalin	e3bn9A1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
B [auth C]	PID	e3bn9C1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: PID	ECOD (v294.1)
E	Lipocalin	e3bn9E1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
C [auth D]	Copper-bind	e3bn9D1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
F	Copper-bind	e3bn9F1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
D [auth A]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	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
B [auth C], E	E2 Fab	L-KAPPA	Homo sapiens (human)	IGKV1-1201, IGKV1D-1201, IGKV1-1202, IGKV1-3901, IGKV1D-3901, IGKV1D-1202, IGKJ201, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)
C [auth D], F	E2 Fab	VH-CH1	Homo sapiens (human)	IGHV3-2304, IGHJ301, IGHJ302, IGHJ501, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth C], E	Light Chain	IGKV1	Kappa	membrane-type serine protease 1	SAbDab (2026-03-27)
C [auth D], F	Heavy Chain	IGHV3	-	membrane-type serine protease 1	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], D [auth A]	PF00089	Trypsin (Trypsin)	Trypsin		Domain
C [auth D], F	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], D [auth A]	Membrane-type serine protease 1	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure epidermal cell differentiation cellular developmental process epidermis development animal organ development epithelial cell differentiation skin development cell differentiation keratinocyte differentiation cellular process catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process cell differentiation involved in embryonic placenta development epithelial cell differentiation involved in embryonic placenta development reproductive process cell development labyrinthine layer development developmental process involved in reproduction cell morphogenesis embryonic placenta development epithelial cell morphogenesis epithelial cell morphogenesis involved in placental branching embryonic organ development placenta development branching involved in labyrinthine layer morphogenesis in utero embryonic development embryonic placenta morphogenesis labyrinthine layer morphogenesis epithelial cell development morphogenesis of a branching structure morphogenesis of a branching epithelium proteolysis	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane
B [auth C], E	E2 Fab Light Chain	-	-	-
C [auth D], F	E2 Fab Heavy Chain	protein-containing complex binding protein binding binding signaling receptor binding immunoglobulin receptor binding Fc-gamma receptor I complex binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus immunoglobulin mediated immune response adaptive immune response immune effector process type II hypersensitivity immune system process type IIa hypersensitivity B cell mediated immunity cellular process inflammatory response cell killing cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway complement-dependent cytotoxicity biological process involved in interspecies interaction between organisms response to other organism antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus	cellular anatomical structure extracellular region blood microparticle protein-containing complex extracellular protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cellular anatomical structure extracellular region blood microparticle protein-containing complex extracellular protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], D [auth A]	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A [auth B], D [auth A]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth B], D [auth A]	IPR017051	Peptidase S1A, matripase	Family
A [auth B], D [auth A]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth B], D [auth A]	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
A [auth B], D [auth A]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth B], D [auth A]	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
A [auth B], D [auth A]	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A [auth B], D [auth A]	IPR036364	SEA domain superfamily	Homologous Superfamily
A [auth B], D [auth A]	IPR000859	CUB domain	Domain
A [auth B], D [auth A]	IPR000082	SEA domain	Domain
A [auth B], D [auth A]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth B], D [auth A]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
C [auth D], F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth D], F	IPR050380	Immune Recognition and Response Modulators	Family
C [auth D], F	IPR003597	Immunoglobulin C1-set	Domain
C [auth D], F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth D], F	IPR007110	Immunoglobulin-like domain	Domain
C [auth D], F	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], D [auth A]	Pharos: Q9Y5Y6	autosomal recessive congenital ichthyosis 11 Netherton syndrome Liver Cirrhosis, Experimental prostate cancer cystic fibrosis ichthyosis linearis circumflexa malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis atopic eczema ductal breast carcinoma in situ interstitial cystitis lung adenocarcinoma pancreatic ductal adenocarcinoma autosomal recessive congenital ichthyosis 11 Netherton syndrome Liver Cirrhosis, Experimental prostate cancer cystic fibrosis ichthyosis linearis circumflexa malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis atopic eczema ductal breast carcinoma in situ interstitial cystitis lung adenocarcinoma pancreatic ductal adenocarcinoma hypotrichosis invasive ductal breast carcinoma lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma
C [auth D], F	Pharos: P01857	B-cell chronic lymphocytic leukemia myositis polycystic ovary syndrome plasma cell myeloma plasma cell neoplasm Sclerocystic Ovaries acquired idiopathic inflammatory myopathy lung adenocarcinoma ovarian cancer peripheral neuropathy Sjogren syndrome amyloidosis breast cancer medulloblastoma nasopharyngeal carcinoma B-cell chronic lymphocytic leukemia myositis polycystic ovary syndrome plasma cell myeloma plasma cell neoplasm Sclerocystic Ovaries acquired idiopathic inflammatory myopathy lung adenocarcinoma ovarian cancer peripheral neuropathy Sjogren syndrome amyloidosis breast cancer medulloblastoma nasopharyngeal carcinoma periodontitis interstitial cystitis myeloid neoplasm osteosarcoma peripheral nervous system disease

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.