6AC9

Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6ac9a_	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	d6ac9b_	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	d6ac9c_	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	d6ac9d_	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)

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)	8080857	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080857	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080857	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080857	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	Pkinase_Tyr	e6ac9A1	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: Pkinase_Tyr	ECOD (1.6)
B	Pkinase_Tyr	e6ac9B1	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: Pkinase_Tyr	ECOD (1.6)
C	Pkinase_Tyr	e6ac9C1	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: Pkinase_Tyr	ECOD (1.6)
D	Pkinase_Tyr	e6ac9D1	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: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	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	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
A, B, C, D	Serine/threonine-protein kinase VRK1	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding histone binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor histone modifying activity histone kinase activity histone H2AX kinase activity kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding histone binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor histone modifying activity histone kinase activity histone H2AX kinase activity 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 kinase binding enzyme binding protein kinase binding protein serine/threonine kinase activity DNA binding protein-containing complex binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding histone H3T3 kinase activity histone H3 kinase activity histone H3S10 kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component disassembly Golgi inheritance organelle inheritance Golgi disassembly cellular component organization organelle organization organelle disassembly cellular component organization or biogenesis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component disassembly Golgi inheritance organelle inheritance Golgi disassembly cellular component organization organelle organization organelle disassembly cellular component organization or biogenesis Golgi organization endomembrane system organization cell division membrane organization nuclear membrane disassembly mitotic cell cycle membrane disassembly nuclear membrane organization mitotic nuclear membrane disassembly nucleus organization mitotic cell cycle process nuclear envelope organization cell cycle cell cycle process developmental process multicellular organismal process regulation of biological process regulation of cell motility regulation of cellular process neuron migration cellular developmental process biological regulation nervous system development regulation of neuron migration generation of neurons neurogenesis multicellular organism development cell differentiation regulation of locomotion anatomical structure development regulation of cell migration cell migration cell motility locomotion system development signaling signal transduction cell communication nuclear body organization Cajal body organization protein phosphorylation protein autophosphorylation phosphorylation cellular metabolic process primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process protein localization regulation of localization cellular localization protein localization to chromatin regulation of protein localization positive regulation of biological process localization protein localization to chromosome regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle positive regulation of protein localization positive regulation of protein localization to chromatin regulation of protein localization to chromatin positive regulation of cellular process plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development neuron differentiation neuron development chromatin organization chromatin remodeling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system Golgi stack cytoplasm cytosol nucleoplasm chromatin chromosome Cajal body 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	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR050235	Casein Kinase 1 Ser/Thr Protein Kinase	Family
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q99986	intellectual disability pontocerebellar hypoplasia type 1A pontocerebellar hypoplasia pontocerebellar hypoplasia type 1 acute myeloid leukemia Cerebellar Hypoplasia lung cancer neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor lymphoplasmacytic lymphoma oligodendroglioma pituitary cancer large cell medulloblastoma medulloblastoma intellectual disability pontocerebellar hypoplasia type 1A pontocerebellar hypoplasia pontocerebellar hypoplasia type 1 acute myeloid leukemia Cerebellar Hypoplasia lung cancer neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor lymphoplasmacytic lymphoma oligodendroglioma pituitary cancer large cell medulloblastoma medulloblastoma microcephaly pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.