4OGY

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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	d4ogya_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4ogyb_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d4ogyh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d4ogym_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d4ogyl2	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)
D [auth L]	d4ogyl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth N]	d4ogyn2	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)
F [auth N]	d4ogyn1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (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	Trypsin_1	e4ogyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
B	Trypsin_1	e4ogyB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
C [auth H]	C1-set_1	e4ogyH1	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)
C [auth H]	V-set_12	e4ogyH2	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)
E [auth M]	C1-set_1	e4ogyM1	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 M]	V-set_12	e4ogyM2	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 L]	C1-set_4	e4ogyL1	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)
D [auth L]	V-set	e4ogyL2	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)
F [auth N]	C1-set_4	e4ogyN1	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)
F [auth N]	V-set	e4ogyN2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth N]	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
C [auth H], E [auth M]	DX-2930	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-2303, IGHV3-23D01, IGHJ302, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202444-0)
D [auth L], F [auth N]	DX-2930	L-KAPPA	Homo sapiens (human)	IGKV1-503, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202444-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], E [auth M]	Heavy Chain	IGHV3	-	plasma kallikrein	SAbDab (2024-11-08)
D [auth L], F [auth N]	Light Chain	IGKV1	Kappa	plasma kallikrein	SAbDab (2024-11-08)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
C [auth H], E [auth M]	Lanadelumab	KLKB1	Therapeutic SAbDab (2024-11-08)
D [auth L], F [auth N]	Lanadelumab	KLKB1	Therapeutic SAbDab (2024-11-08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain
C [auth H], E [auth M]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C [auth H], E [auth M]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
D [auth L], F [auth N]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
D [auth L], F [auth N]	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, B	Plasma kallikrein	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 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 regulation of response to external stimulus negative regulation of biological process positive regulation of biological process 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 regulation of response to external stimulus negative regulation of biological process positive regulation of biological process regulation of coagulation regulation of response to wounding regulation of response to stress regulation of multicellular organismal process regulation of hemostasis regulation of biological process negative regulation of response to stimulus regulation of blood coagulation negative regulation of wound healing negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding positive regulation of fibrinolysis negative regulation of hemostasis fibrinolysis regulation of fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process zymogen activation cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process plasminogen activation regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of protein processing regulation of primary metabolic process kinin cascade positive regulation of metabolic process regulation of proteolysis positive regulation of macromolecule metabolic process protein activation cascade regulation of protein metabolic process regulation of cellular metabolic process regulation of inflammatory response regulation of gene expression positive regulation of proteolysis regulation of protein processing regulation of acute inflammatory response regulation of macromolecule biosynthetic process inflammatory response regulation of metabolic process regulation of defense response positive regulation of protein metabolic process activation of plasma proteins involved in acute inflammatory response positive regulation of cellular metabolic process plasma kallikrein-kinin cascade positive regulation of biosynthetic process Factor XII activation acute inflammatory response positive regulation of cellular process regulation of biosynthetic process defense response regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of gene expression positive regulation of cellular biosynthetic process	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane
C [auth H], E [auth M]	DX-2930 HEAVY CHAIN	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process	extracellular region extracellular space cellular anatomical entity blood microparticle cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex
D [auth L], F [auth N]	DX-2930 LIGHT CHAIN	-	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000177	Apple domain	Domain
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, B	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, B	IPR001254	Serine proteases, trypsin domain	Domain
A, B	IPR003609	PAN/Apple domain	Domain
A, B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
C [auth H], E [auth M]	IPR050199	Immunoglobulin Heavy Variable	Family
C [auth H], E [auth M]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], E [auth M]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H], E [auth M]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H], E [auth M]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth H], E [auth M]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth H], E [auth M]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H], E [auth M]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D [auth L], F [auth N]	IPR003597	Immunoglobulin C1-set	Domain
D [auth L], F [auth N]	IPR050150	Immunoglobulin Variable Light Chain	Family
D [auth L], F [auth N]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth L], F [auth N]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth L], F [auth N]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth L], F [auth N]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth L], F [auth N]	IPR007110	Immunoglobulin-like domain	Domain
D [auth L], F [auth N]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P03952	carotid artery thrombosis inherited prekallikrein deficiency prekallikrein deficiency pulmonary embolism angioedema Common Carotid Artery Thrombosis hereditary angioedema lung cancer ovarian cancer lung carcinoma vascular disease cerebrovascular disorder osteosarcoma thrombotic disease