4C58

Structure of GAK kinase in complex with nanobody (NbGAK_4)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8098110	3000066	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)
B	PF07686	e4c58B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
A	PF00069	e4c58A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PF00069	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	cyclin-g-associated kinase	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	nanobody	-	-	-
A	Cyclin-G-associated kinase	clathrin binding protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein-folding chaperone binding adenyl ribonucleotide binding clathrin binding protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein-folding chaperone binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity	protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization cellular process localization within membrane protein localization to membrane cellular component disassembly clathrin coat disassembly transport protein-containing complex organization protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization cellular process localization within membrane protein localization to membrane cellular component disassembly clathrin coat disassembly transport protein-containing complex organization protein-containing complex disassembly establishment of localization vesicle-mediated transport vesicle uncoating cellular component organization cellular component organization or biogenesis protein depolymerization regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell projection organization system development developmental process regulation of biological process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization biological regulation nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization import into cell clathrin-dependent endocytosis receptor-mediated endocytosis endocytosis post-Golgi vesicle-mediated transport intracellular transport lysosomal transport Golgi to vacuole transport cytosolic transport establishment of localization in cell vacuolar transport Golgi to lysosome transport Golgi vesicle transport cell cycle organelle organization endoplasmic reticulum organization endomembrane system organization organonitrogen compound metabolic process cellular biosynthetic process chaperone cofactor-dependent protein refolding cellular metabolic process primary metabolic process gene expression chaperone-mediated protein folding macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process protein metabolic process macromolecule metabolic process 'de novo' protein folding 'de novo' post-translational protein folding clathrin coat assembly cellular component biogenesis cellular component assembly protein-containing complex assembly protein localization to Golgi apparatus protein localization to organelle phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process synaptic vesicle uncoating synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling synaptic vesicle endocytosis regulation of clathrin coat assembly regulation of cellular component biogenesis regulation of protein-containing complex assembly Golgi organization	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane membrane-bounded organelle organelle vesicle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane membrane-bounded organelle organelle vesicle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle clathrin-coated vesicle coated vesicle cytoplasm cytosol presynapse synapse Golgi apparatus endomembrane system perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001623	DnaJ domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR029023	Tensin-type phosphatase domain	Domain
A	IPR014020	Tensin phosphatase, C2 domain	Domain
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR036869	Chaperone J-domain superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR035892	C2 domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O14976	Parkinson disease primary myelofibrosis rheumatoid arthritis acute myeloid leukemia Chronic Myelocytic Leukemia Accelerated Phase myositis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis systemic lupus erythematosus pancreatic adenocarcinoma primary biliary cholangitis renal cell carcinoma systemic sclerosis bone disease Parkinson disease primary myelofibrosis rheumatoid arthritis acute myeloid leukemia Chronic Myelocytic Leukemia Accelerated Phase myositis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis systemic lupus erythematosus pancreatic adenocarcinoma primary biliary cholangitis renal cell carcinoma systemic sclerosis bone disease gastrointestinal stromal tumor non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.