5D7V

Crystal structure of PTK6 kinase domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5d7va1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5d7va3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5d7va2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5d7vb1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5d7vb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5d7vb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5d7vc1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5d7vc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5d7vc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5d7vd1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5d7vd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5d7vd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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)	8069191	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8069191	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8069191	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8069191	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)
A	PF07714	e5d7vA1	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: PF07714	ECOD (1.6)
B	PF07714	e5d7vB1	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: PF07714	ECOD (1.6)
C	PF07714	e5d7vC1	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: PF07714	ECOD (1.6)
D	PF07714	e5d7vD1	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: PF07714	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07714	Protein tyrosine and serine/threonine kinase (PK_Tyr_Ser-Thr)	Protein tyrosine and serine/threonine kinase	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosph ...	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [1]; Serine/threonine-protein kinases, tyrosine-protein kinases, and dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins). This entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include the catalytic domain of dual specificity kinases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Protein-tyrosine kinase 6	protein binding binding signaling receptor 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 protein binding binding signaling receptor 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding non-membrane spanning protein tyrosine kinase activity identical protein binding	regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus cell surface receptor signaling pathway via STAT response to stimulus signaling peptidyl-tyrosine modification regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus cell surface receptor signaling pathway via STAT response to stimulus signaling peptidyl-tyrosine modification cell communication organic substance metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process signal transduction protein modification process phosphorus metabolic process tyrosine phosphorylation of STAT protein organonitrogen compound metabolic process protein phosphorylation cell surface receptor signaling pathway phosphorylation cellular metabolic process primary metabolic process macromolecule modification metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT developmental process cellular developmental process cell differentiation multicellular organismal process epithelium development digestive system development intestinal epithelial cell differentiation tube development tissue development digestive tract development epithelial cell differentiation multicellular organism development anatomical structure development columnar/cuboidal epithelial cell differentiation system development negative regulation of protein tyrosine kinase activity regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of transferase activity negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process negative regulation of protein modification process negative regulation of protein metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of molecular function regulation of protein tyrosine kinase activity regulation of kinase activity negative regulation of protein phosphorylation regulation of phosphorus metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of peptidyl-tyrosine phosphorylation regulation of peptidyl-tyrosine phosphorylation negative regulation of molecular function regulation of macromolecule metabolic process regulation of protein kinase activity negative regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation positive regulation of DNA replication nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process DNA metabolic process nucleic acid metabolic process organic cyclic compound metabolic process DNA replication positive regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus response to organic substance response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid response to chemical cellular response to lipid cellular response to organic substance positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling regulation of response to stimulus ERBB signaling pathway regulation of cell communication positive regulation of signaling cell migration cell motility protein autophosphorylation regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cell projection organization cell development neuron projection development cellular component organization neurogenesis neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization ERBB2 signaling pathway positive regulation of phosphorylation positive regulation of phosphate metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of tyrosine phosphorylation of STAT protein positive regulation of tyrosine phosphorylation of STAT protein regulation of growth negative regulation of growth growth	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen extrinsic component of plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane side of membrane ruffle cell projection cell leading edge plasma membrane bounded cell projection nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B, C, D	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B, C, D	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR000980	SH2 domain	Domain
A, B, C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR035846	PTK6, SH2 domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR001452	SH3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q13882	pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida B-cell chronic lymphocytic leukemia Chronic Myelocytic Leukemia Accelerated Phase ductal breast carcinoma in situ lung adenocarcinoma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma Waldenstrom macroglobulinemia interstitial cystitis lymphoplasmacytic lymphoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm cystic fibrosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida B-cell chronic lymphocytic leukemia Chronic Myelocytic Leukemia Accelerated Phase ductal breast carcinoma in situ lung adenocarcinoma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma Waldenstrom macroglobulinemia interstitial cystitis lymphoplasmacytic lymphoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm cystic fibrosis invasive ductal breast carcinoma macroglobulinemia mantle cell lymphoma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	CXM	Parent Component: MET RESID: AA0363 , AA0493 PSI-MOD : N-carboxy-L-methionine MOD:00368 , N-(dihydroxymethyl)-L-methionine (fMet) MOD:01446 , N-(dihydroxymethyl)-L-methionine (Met) MOD:01447

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.