2WUB | pdb_00002wub

Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody Fab40.deltaTrp

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G [auth Q]	d2wubq2	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)
G [auth Q]	d2wubq1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d2wubl2	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 L]	d2wubl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth R]	d2wubr_	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 H]	d2wubh_	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth Q]	C1-set	e2wubQ1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
F [auth L]	C1-set	e2wubL1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
H [auth R]	C1-set	e2wubR1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
E [auth H]	C1-set	e2wubH1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
C	C1-set	e2wubC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
A	Bac_rhodopsin	e2wubA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: Bac_rhodopsin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth Q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth R]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	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
F [auth L], G [auth Q]	Fab 40.DELTATRP	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKV1-1302, IGKV1D-1302, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)
E [auth H], H [auth R]	Fab 40.DELTATRP	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, 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
F [auth L], G [auth Q]	Light Chain	IGKV1	Kappa	hepatocyte growth factor activator long chain	SAbDab (2026-03-27)
E [auth H], H [auth R]	Heavy Chain	IGHV3	-	hepatocyte growth factor activator long chain	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth L], G [auth Q]	FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN	-	-	-
E [auth H], H [auth R]	FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN	-	-	-
B, D	HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN	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 proteolysis metabolic process cellular 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 proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol rough endoplasmic reticulum membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system extracellular region
A, C	HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN	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 proteolysis metabolic process cellular 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 proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol rough endoplasmic reticulum membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR036943	Fibronectin type II domain superfamily	Homologous Superfamily
B, D	IPR018056	Kringle, conserved site	Conserved Site
B, D	IPR014394	Coagulation factor XII/hepatocyte growth factor activator	Family
B, D	IPR000562	Fibronectin type II domain	Domain
B, D	IPR000742	EGF-like domain	Domain
B, D	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B, D	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
B, D	IPR013806	Kringle-like fold	Homologous Superfamily
B, D	IPR038178	Kringle superfamily	Homologous Superfamily
B, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, D	IPR000083	Fibronectin, type I	Domain
B, D	IPR001314	Peptidase S1A, chymotrypsin family	Family
B, D	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B, D	IPR001254	Serine proteases, trypsin domain	Domain
B, D	IPR050127	Serine Proteases (Peptidase S1 Family)	Family
B, D	IPR000001	Kringle	Domain
A, C	IPR036943	Fibronectin type II domain superfamily	Homologous Superfamily
A, C	IPR018056	Kringle, conserved site	Conserved Site
A, C	IPR014394	Coagulation factor XII/hepatocyte growth factor activator	Family
A, C	IPR000562	Fibronectin type II domain	Domain
A, C	IPR000742	EGF-like domain	Domain
A, C	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A, C	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, C	IPR013806	Kringle-like fold	Homologous Superfamily
A, C	IPR038178	Kringle superfamily	Homologous Superfamily
A, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, C	IPR000083	Fibronectin, type I	Domain
A, C	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, C	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, C	IPR001254	Serine proteases, trypsin domain	Domain
A, C	IPR050127	Serine Proteases (Peptidase S1 Family)	Family
A, C	IPR000001	Kringle	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q04756	cystic fibrosis Liver carcinoma heart disease hepatocellular carcinoma
A, C	Pharos: Q04756	cystic fibrosis Liver carcinoma heart disease hepatocellular carcinoma