4K3J | pdb_00004k3j

Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta

External Resource: Annotation

Domain Annotation: SCOP2 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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Sema domain-like	8039465	3000180	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Plexin repeat-like	8039466	3000415	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8042342	3000114	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)
D [auth L]	PNP_UDP_1	e4k3jL1	A: alpha bundles	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: PNP_UDP_1	ECOD (develop294)
C [auth H]	PNP_UDP_1	e4k3jH1	A: alpha bundles	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: PNP_UDP_1	ECOD (develop294)
B	PNP_UDP_1	e4k3jB1	A: alpha bundles	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: PNP_UDP_1	ECOD (develop294)
A	PNP_UDP_1	e4k3jA1	A: alpha bundles	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: PNP_UDP_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	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
D [auth L]	OA5D5, anti-MET	L-KAPPA	Humanized (humanized)	IGKV1D-1301, IGKV1-1302, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
C [auth H]	OA5D5, anti-MET	VH-CH1	Humanized (humanized)	IGHV3-7401, IGHV3-7402, IGHV3-7403, IGHV3-2304, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L]	Light Chain	IGKV1	Kappa	hepatocyte growth factor beta chain	SAbDab (2026-03-20)
C [auth H]	Heavy Chain	IGHV3	-	hepatocyte growth factor beta chain	SAbDab (2026-03-20)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
D [auth L]	Onartuzumab	MET/HGFR	Therapeutic SAbDab (2026-03-20)
C [auth H]	Onartuzumab	MET/HGFR	Therapeutic SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01437	Plexin repeat (PSI)	Plexin repeat	-	Family
B	PF01403	Sema domain (Sema)	Sema domain	-	Repeat
A	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L]	Onartuzumab Fab light chain	-	-	-
C [auth H]	Onartuzumab Fab heavy chain	-	-	-
B	Hepatocyte growth factor beta chain	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity protein phosphatase binding phosphatase binding protein binding binding enzyme binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity protein phosphatase binding phosphatase binding protein binding binding enzyme binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding molecular function activator activity molecular function regulator activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity hepatocyte growth factor receptor activity identical protein binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation cell morphogenesis endothelial cell development anatomical structure morphogenesis epithelial cell development endothelial cell morphogenesis epithelial cell morphogenesis cell differentiation cellular process tube development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue morphogenesis tube morphogenesis morphogenesis of a branching structure epithelial tube morphogenesis morphogenesis of a branching epithelium regulation of hydrogen peroxide-mediated programmed cell death cellular response to stimulus regulation of cellular process response to stimulus programmed cell death in response to reactive oxygen species cellular response to oxidative stress negative regulation of biological process regulation of programmed cell death cellular response to chemical stress negative regulation of hydrogen peroxide-mediated programmed cell death cellular response to reactive oxygen species hydrogen peroxide-mediated programmed cell death cellular response to stress response to stress negative regulation of cellular process regulation of biological process negative regulation of programmed cell death biological regulation response to oxygen-containing compound cell death cellular response to oxygen-containing compound response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus response to chemical programmed cell death positive chemotaxis chemotaxis taxis response to external stimulus locomotion nervous system development generation of neurons neurogenesis neuron differentiation cell surface receptor signaling pathway signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication hepatocyte growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of postsynaptic membrane potential system process chemical synaptic transmission, postsynaptic synaptic signaling regulation of biological quality trans-synaptic signaling nervous system process cell-cell signaling chemical synaptic transmission anterograde trans-synaptic signaling excitatory postsynaptic potential regulation of membrane potential pancreas development positive regulation of locomotion regulation of cell motility regulation of response to external stimulus endothelial cell migration positive regulation of biological process positive regulation of chemotaxis positive regulation of cell migration positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration positive regulation of endothelial cell chemotaxis regulation of endothelial cell migration cell migration endothelial cell chemotaxis cell motility positive regulation of cellular process cell chemotaxis regulation of endothelial cell chemotaxis regulation of chemotaxis regulation of response to stimulus regulation of locomotion positive regulation of endothelial cell migration semaphorin-plexin signaling pathway negative regulation of catabolic process catabolic process negative regulation of metabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of autophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription	cellular anatomical structure membrane cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region cell surface protein-containing complex receptor complex extracellular region postsynapse synapse cell junction
A	Hepatocyte growth factor	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity chemoattractant activity identical protein binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development cellular process cell cycle mitotic cell cycle myoblast proliferation cell population proliferation developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development cellular process cell cycle mitotic cell cycle myoblast proliferation cell population proliferation interleukin-6 production regulation of cellular process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death cellular response to stimulus extrinsic apoptotic signaling pathway via death domain receptors response to stimulus signaling negative regulation of signaling regulation of signal transduction extrinsic apoptotic signaling pathway negative regulation of cell communication cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of extrinsic apoptotic signaling pathway via death domain receptors negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication regulation of apoptotic signaling pathway regulation of hydrogen peroxide-mediated programmed cell death programmed cell death in response to reactive oxygen species cellular response to oxidative stress cellular response to chemical stress negative regulation of hydrogen peroxide-mediated programmed cell death cellular response to reactive oxygen species hydrogen peroxide-mediated programmed cell death cellular response to stress response to stress response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus response to chemical regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of biological process intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell surface receptor protein tyrosine kinase signaling pathway hepatocyte growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway regulation of cellular component organization apoptotic mitochondrial changes regulation of release of cytochrome c from mitochondria cellular component organization negative regulation of release of cytochrome c from mitochondria cellular component organization or biogenesis mitochondrion organization negative regulation of cellular component organization regulation of organelle organization organelle organization release of cytochrome c from mitochondria negative regulation of organelle organization regulation of mitochondrion organization positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade mesenchymal-epithelial cell signaling regulation of developmental process branching involved in salivary gland morphogenesis gland morphogenesis salivary gland morphogenesis regulation of branching involved in salivary gland morphogenesis regulation of morphogenesis of an epithelium animal organ morphogenesis regulation of anatomical structure morphogenesis regulation of morphogenesis of a branching structure epithelium development regulation of animal organ morphogenesis morphogenesis of an epithelium salivary gland development cell-cell signaling tissue development regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling tissue morphogenesis anatomical structure morphogenesis morphogenesis of a branching structure exocrine system development morphogenesis of a branching epithelium cell chemotaxis chemotaxis taxis cell migration cell motility locomotion cell morphogenesis epithelial cell proliferation cellular developmental process cell differentiation mesenchyme development mesenchymal cell differentiation epithelial to mesenchymal transition p38MAPK cascade regulation of p38MAPK cascade regulation of osteoblast differentiation regulation of cell differentiation osteoblast differentiation positive regulation of developmental process positive regulation of osteoblast differentiation ossification positive regulation of cell differentiation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration interleukin-10 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of interleukin-10 production positive regulation of interleukin-10 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production negative regulation of catabolic process catabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of autophagy process utilizing autophagic mechanism regulation of DNA biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process regulation of nucleobase-containing compound metabolic process positive regulation of DNA biosynthetic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of DNA metabolic process DNA biosynthetic process regulation of DNA metabolic process cellular response to endogenous stimulus response to hepatocyte growth factor cellular response to growth factor stimulus cellular response to hepatocyte growth factor stimulus response to endogenous stimulus response to growth factor positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription muscle cell proliferation skeletal muscle cell proliferation striated muscle cell proliferation	cellular anatomical structure membrane extracellular region membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure membrane extracellular region membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle cytoplasm platelet alpha granule vesicle platelet alpha granule lumen extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR002909	IPT domain	Domain
B	IPR008266	Tyrosine-protein kinase, active site	Active Site
B	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
B	IPR016201	PSI domain	Domain
B	IPR016244	Tyrosine-protein kinase, HGF/MSP receptor	Family
B	IPR000719	Protein kinase domain	Domain
B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR002165	Plexin repeat	Repeat
B	IPR031148	Plexin family	Family
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR036352	Sema domain superfamily	Homologous Superfamily
B	IPR001627	Sema domain	Domain
A	IPR018056	Kringle, conserved site	Conserved Site
A	IPR003609	PAN/Apple domain	Domain
A	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A	IPR013806	Kringle-like fold	Homologous Superfamily
A	IPR038178	Kringle superfamily	Homologous Superfamily
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A	IPR050759	Serine proteases and regulators with kringle domains	Family
A	IPR001314	Peptidase S1A, chymotrypsin family	Family
A	IPR027284	Hepatocyte growth factor	Family
A	IPR024174	Hepatocyte growth factor/Macrophage stimulatory protein	Family
A	IPR001254	Serine proteases, trypsin domain	Domain
A	IPR000001	Kringle	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P08581	squamous cell carcinoma hepatocellular carcinoma glioblastoma renal cell carcinoma neuroblastoma osteosarcoma papillary renal cell carcinoma acute myeloid leukemia non-small cell lung carcinoma osteofibrous dysplasia ovarian cancer cancer nonsyndromic genetic deafness esophageal cancer autosomal recessive nonsyndromic deafness 97 squamous cell carcinoma hepatocellular carcinoma glioblastoma renal cell carcinoma neuroblastoma osteosarcoma papillary renal cell carcinoma acute myeloid leukemia non-small cell lung carcinoma osteofibrous dysplasia ovarian cancer cancer nonsyndromic genetic deafness esophageal cancer autosomal recessive nonsyndromic deafness 97 giant cell glioblastoma granular cell carcinoma sarcomatoid renal cell carcinoma Hepatitis, Chronic adenocarcinoma juvenile pilocytic astrocytoma lung cancer fibrillary astrocytoma protoplasmic astrocytoma schizophrenia collecting duct carcinoma astrocytic tumor pilocytic astrocytoma gastric cancer prostate cancer gemistocytic astrocytoma carcinoma sarcomatoid carcinoma childhood cerebral astrocytoma sinusitis chromophobe renal cell carcinoma subependymal giant cell astrocytoma tubular adenocarcinoma anaplastic astrocytoma malignant mesothelioma benign neoplasm of stomach malignant pancreatic neoplasm breast disease renal carcinoma hereditary diffuse gastric adenocarcinoma interstitial lung disease adrenal medulla cancer cribriform carcinoma of breast attention deficit hyperactivity disorder, inattentive type pancreatic intraductal papillary-mucinous neoplasm esophageal adenocarcinoma benign neoplasm of adrenal gland primitive neuroectodermal tumor gastric neoplasm breast cancer medullary thyroid gland carcinoma head and neck squamous cell carcinoma cerebral astrocytoma hepatoblastoma cholangiocarcinoma stomach carcinoma in situ tuberculosis hereditary papillary renal cell carcinoma ulcerative colitis large cell medulloblastoma ovarian neoplasm atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia lung carcinoma malignant colon neoplasm breast carcinoma psoriasis medulloblastoma hepatitis neoplasm of esophagus non-alcoholic fatty liver disease clear cell renal carcinoma intellectual disability oligodendroglioma colorectal adenocarcinoma undifferentiated carcinoma invasive ductal breast carcinoma cribriform carcinoma liver cancer astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma diffuse astrocytoma lung benign neoplasm autism lung disease Barrett esophagus pituitary cancer gastric carcinoma
A	Pharos: P14210	autosomal recessive nonsyndromic deafness 39 pilocytic astrocytoma squamous cell carcinoma nonsyndromic genetic deafness pancreatitis subependymal giant cell astrocytoma neuroblastoma Barrett esophagus acute myeloid leukemia cardiomyopathy juvenile pilocytic astrocytoma Copper-Overload Cirrhosis liver cancer protoplasmic astrocytoma diabetic autonomic neuropathy autosomal recessive nonsyndromic deafness 39 pilocytic astrocytoma squamous cell carcinoma nonsyndromic genetic deafness pancreatitis subependymal giant cell astrocytoma neuroblastoma Barrett esophagus acute myeloid leukemia cardiomyopathy juvenile pilocytic astrocytoma Copper-Overload Cirrhosis liver cancer protoplasmic astrocytoma diabetic autonomic neuropathy diabetic neuropathy vascular disease pulmonary fibrosis acute liver failure diabetic polyneuropathy malignant mesothelioma fibrillary astrocytoma anaplastic astrocytoma gemistocytic astrocytoma childhood cerebral astrocytoma cirrhosis of liver Parkinson disease polyomavirus infectious disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia deafness, autosomal recessive liver disease lung cancer malignant glioma medulloblastoma adrenal cortex carcinoma gastric carcinoma myocardial ischemia astrocytoma (excluding glioblastoma) hepatocellular carcinoma ovarian cancer cancer idiopathic interstitial pneumonia cerebral astrocytoma invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous carcinoma keratoconus coronary artery disease plasma cell myeloma liver neoplasm lung disease rheumatoid arthritis tuberculosis hepatitis oligodendroglioma interstitial cystitis ischemia reperfusion injury pancreatic intraductal papillary-mucinous neoplasm large cell medulloblastoma malignant ependymoma Sjogren syndrome diffuse astrocytoma MALT lymphoma adrenal cortex adenoma astrocytic tumor thrombotic disease ulcerative colitis non-small cell lung carcinoma osteosarcoma breast cancer