4IIR | pdb_00004iir

Crystal Structure of AMPPNP-bound Human PRPF4B 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)
B	d4iirb_	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	d4iira_	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)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079157	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079157	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		e4iirB1	A: beta-propeller-like	X: beta-propeller	H: 6-bladed	T: PNP_UDP_1	F:	ECOD (20:10:01)
A		e4iirA1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: LysR_substrate	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Serine/threonine-protein kinase PRP4 homolog	binding 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 binding 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 protein serine/threonine 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 RNA binding nucleic acid binding protein serine kinase activity	regulation of localization establishment of protein localization cellular localization regulation of cellular process regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of biological process positive regulation of establishment of protein localization positive regulation of protein transport localization establishment of localization in cell regulation of localization establishment of protein localization cellular localization regulation of cellular process regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of biological process positive regulation of establishment of protein localization positive regulation of protein transport localization establishment of localization in cell positive regulation of intracellular transport intracellular protein localization nuclear export regulation of protein export from nucleus positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of transport biological regulation regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport regulation of protein transport protein export from nucleus positive regulation of protein export from nucleus establishment of localization positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport cellular process intracellular protein transport RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing cellular response to stimulus regulation of cell cycle phase transition response to stimulus negative regulation of biological process spindle checkpoint signaling negative regulation of cell cycle regulation of signal transduction regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication regulation of cell cycle checkpoint negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction cell cycle mitotic sister chromatid separation chromosome segregation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling negative regulation of cellular component organization regulation of cell cycle process regulation of spindle checkpoint sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation mitotic cell cycle process regulation of response to stimulus regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of cellular component organization regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle regulation of mitotic spindle checkpoint signaling regulation of mitotic cell cycle spindle assembly checkpoint spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle regulation of intracellular signal transduction negative regulation of cellular process mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition cellular component organization or biogenesis regulation of cell cycle negative regulation of chromosome separation cell cycle process mitotic nuclear division regulation of signaling negative regulation of mitotic cell cycle phase transition organelle fission chromosome organization negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling organelle organization nuclear division negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle regulation of cell communication metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition ribonucleoprotein complex biogenesis spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly protein-containing complex organization spliceosomal snRNP assembly hippo signaling positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction positive regulation of hippo signaling regulation of hippo signaling positive regulation of signaling	intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome membrane-bounded organelle intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen nuclear ribonucleoprotein granule nuclear lumen catalytic step 2 spliceosome protein-containing complex catalytic complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050494	Serine/threonine and dual-specificity kinase	Family
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR044092	Serine/threonine-protein PRP4, catalytic domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13523	osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy amyotrophic lateral sclerosis dermatomyositis glioblastoma Interstitial fibrosis lung adenocarcinoma non-small cell lung carcinoma ovarian cancer Pick disease psoriasis astrocytic tumor Down syndrome hereditary spastic paraplegia osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy amyotrophic lateral sclerosis dermatomyositis glioblastoma Interstitial fibrosis lung adenocarcinoma non-small cell lung carcinoma ovarian cancer Pick disease psoriasis astrocytic tumor Down syndrome hereditary spastic paraplegia interstitial lung disease malignant ependymoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor Gaucher disease idiopathic pulmonary fibrosis large cell medulloblastoma malignant glioma myopathy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.