2UZY | pdb_00002uzy

Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	L domain-like	8036334	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8055069	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L domain-like	8036334	3001010	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8055069	3000070	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Plexin repeat-like	8039466	3000415	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sema domain-like	8039465	3000180	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Plexin repeat-like	8039466	3000415	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sema domain-like	8039465	3000180	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	LRR_adjacent	e2uzyA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LRR_adjacent	ECOD (1.6)
A	LRR_9	e2uzyA2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_9	ECOD (1.6)
A	Internalin_N	e2uzyA3	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Internalin_N	ECOD (1.6)
C	LRR_adjacent	e2uzyC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LRR_adjacent	ECOD (1.6)
C	LRR_9	e2uzyC2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_9	ECOD (1.6)
C	Internalin_N	e2uzyC3	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Internalin_N	ECOD (1.6)
B	TIG_2	e2uzyB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TIG_2	ECOD (1.6)
B	TIG_1	e2uzyB4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TIG_1	ECOD (1.6)
B	Sema_2	e2uzyB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema_2	ECOD (1.6)
B	PSI_1	e2uzyB2	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PSI_1	ECOD (1.6)
D	TIG_2	e2uzyD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TIG_2	ECOD (1.6)
D	TIG_1	e2uzyD3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TIG_1	ECOD (1.6)
D	Sema_2	e2uzyD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema_2	ECOD (1.6)
D	PSI_1	e2uzyD4	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PSI_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
A	2.60.40.1220	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C	2.60.40.1220	Mainly Beta	Sandwich	Immunoglobulin-like		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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF12354	Bacterial adhesion/invasion protein N terminal (Internalin_N)	Bacterial adhesion/invasion protein N terminal	This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00560, Pfam:PF08191, Pfam:PF09479. There are two completely conserved residues (I and F) that may be functionally i ...	This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00560, Pfam:PF08191, Pfam:PF09479. There are two completely conserved residues (I and F) that may be functionally important. Internalin mediates bacterial adhesion and invasion of epithelial cells in the human intestine through specific interaction with its host cell receptor E-cadherin. This family is the N terminal of internalin, the cap domain of the protein. The cap domain is conserved between different internalin types. The cap domain does not interact with E cadherin, therefore its function is presumably structural: capping the hydrophobic core.	Domain
A, C	PF12799	Leucine Rich repeats (2 copies) (LRR_4)	Leucine Rich repeats (2 copies)	-	Repeat
A, C	PF08191	LRR adjacent (LRR_adjacent)	LRR adjacent	-	Family
B, D	PF01833	IPT/TIG domain (TIG)	IPT/TIG domain	This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family d ...	This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.	Domain
B, D	PF01437	Plexin repeat (PSI)	Plexin repeat	-	Family
B, D	PF01403	Sema domain (Sema)	Sema domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	INTERNALIN B	binding lipid binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	-	cellular anatomical structure extracellular region cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm
B, D	HEPATOCYTE GROWTH FACTOR RECEPTOR	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 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 transducer activity signaling receptor activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity hepatocyte growth factor receptor activity identical protein binding semaphorin receptor activity molecular function activator activity molecular function regulator activity	developmental process multicellular organismal process epithelium development tube development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis morphogenesis of a branching structure anatomical structure development epithelial tube morphogenesis developmental process multicellular organismal process epithelium development tube development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis morphogenesis of a branching structure anatomical structure development epithelial tube morphogenesis morphogenesis of a branching epithelium establishment of skin barrier skin development skin epidermis development epidermis development animal organ development 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 cellular process programmed cell death negative regulation of thrombin-activated receptor signaling pathway signaling negative regulation of signaling regulation of signal transduction negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication cell communication thrombin-activated receptor signaling pathway signal transduction regulation of G protein-coupled receptor signaling pathway regulation of signaling negative regulation of response to stimulus regulation of thrombin-activated receptor signaling pathway negative regulation of signal transduction regulation of response to stimulus regulation of cell communication G protein-coupled receptor signaling pathway positive chemotaxis chemotaxis taxis response to external stimulus locomotion 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 organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization positive regulation of cellular component organization microtubule cytoskeleton organization positive regulation of biological process cellular component organization cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly microtubule polymerization or depolymerization positive regulation of protein polymerization protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process protein polymerization positive regulation of microtubule polymerization or depolymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of microtubule-based process microtubule polymerization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis regulation of organelle organization organelle organization positive regulation of microtubule polymerization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization microtubule-based process supramolecular fiber organization cytoskeleton organization regulation of microtubule cytoskeleton organization 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 positive regulation of nucleobase-containing compound metabolic process 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 positive regulation of molecular function regulation of molecular function regulation of catalytic activity regulation of binding regulation of hydrolase activity negative regulation of guanyl-nucleotide exchange factor activity negative regulation of molecular function regulation of GTPase activity positive regulation of binding hepaticobiliary system development gland development liver development system development endothelial cell differentiation cellular developmental process endothelium development cell development epithelial cell differentiation cell morphogenesis endothelial cell development epithelial cell development endothelial cell morphogenesis epithelial cell morphogenesis cell differentiation regulation of actin filament-based process regulation of actin filament bundle assembly actin filament bundle organization actin filament-based process stress fiber assembly negative regulation of supramolecular fiber organization regulation of actin filament organization negative regulation of stress fiber assembly actin cytoskeleton organization actomyosin structure organization negative regulation of cellular component organization negative regulation of cytoskeleton organization actin filament organization negative regulation of actin filament bundle assembly regulation of stress fiber assembly negative regulation of organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly nervous system development generation of neurons neurogenesis neuron differentiation regulation of postsynaptic membrane potential system process chemical synaptic transmission, postsynaptic synaptic signaling regulation of biological quality trans-synaptic signaling cell surface receptor signaling pathway 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 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 cell chemotaxis regulation of endothelial cell chemotaxis regulation of chemotaxis regulation of locomotion positive regulation of endothelial cell migration small GTPase-mediated signal transduction negative regulation of Rho protein signal transduction regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction intracellular signal transduction Rho protein signal transduction regulation of intracellular signal transduction intracellular signaling cassette negative regulation of small GTPase mediated signal transduction regulation of Rho protein signal transduction semaphorin-plexin signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway	cellular anatomical structure membrane protein-containing complex receptor complex postsynapse synapse cell junction cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region cell surface extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR025875	Leucine rich repeat 4	Repeat
A, C	IPR025987	GW domain	Domain
A, C	IPR013378	Internalin B-like, B-repeat	Repeat
A, C	IPR001611	Leucine-rich repeat	Repeat
A, C	IPR038200	GW domain superfamily	Homologous Superfamily
A, C	IPR012569	Internalin, Ig-like inter-repeat region	Domain
A, C	IPR024634	Internalin, N-terminal	Domain
A, C	IPR042229	Listeria-Bacteroides repeat domain superfamily	Homologous Superfamily
A, C	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, C	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C	IPR014755	Copper resistance protein CopC/internalin, immunoglobulin-like	Homologous Superfamily
A, C	IPR050836	SDS22/Internalin LRR-containing	Family
B, D	IPR002909	IPT domain	Domain
B, D	IPR008266	Tyrosine-protein kinase, active site	Active Site
B, D	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
B, D	IPR016244	Tyrosine-protein kinase, HGF/MSP receptor	Family
B, D	IPR000719	Protein kinase domain	Domain
B, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, D	IPR031148	Plexin family	Family
B, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D	IPR036352	Sema domain superfamily	Homologous Superfamily
B, D	IPR017441	Protein kinase, ATP binding site	Binding Site
B, D	IPR016201	PSI domain	Domain
B, D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
B, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, D	IPR002165	Plexin repeat	Repeat
B, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B, D	IPR001627	Sema domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	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 lung carcinoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia 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 lung disease autism Barrett esophagus pituitary cancer gastric carcinoma