6S1F | pdb_00006s1f

Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP3

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)
D	d6s1fd_	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	d6s1fc_	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	d6s1fb_	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	d6s1fa_	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)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8077663	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8077663	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8077663	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8077663	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)
D		e6s1fD1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: PSII	F:	ECOD (20:10:01)
C		e6s1fC1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: PSII	F:	ECOD (20:10:01)
B		e6s1fB1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: PSII	F:	ECOD (20:10:01)
A		e6s1fA1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: PSII	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)

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 triphospha ...	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	Receptor-interacting serine/threonine-protein kinase 2	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 binding enzyme binding protease binding caspase binding non-membrane spanning protein tyrosine kinase activity 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 protein serine/threonine kinase activity JUN kinase kinase kinase activity MAP kinase kinase kinase activity identical protein binding signaling receptor binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity LIM domain binding protein domain specific binding protein serine kinase activity protein homodimerization activity protein dimerization activity CARD domain binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of cellular response to stress positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of cellular response to stress positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress intracellular signaling cassette signal transduction positive regulation of stress-activated protein kinase signaling cascade positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of stress-activated MAPK cascade positive regulation of MAPK cascade biological regulation regulation of stress-activated protein kinase signaling cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process positive regulation of signaling cell surface receptor signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide response to chemical cellular response to cytokine stimulus immune response immune system process adaptive immune response positive regulation of T-helper 1 type immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of adaptive immune response T-helper 1 type immune response regulation of T-helper 1 type immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response regulation of immune response regulation of immune system process positive regulation of adaptive immune response positive regulation of immune system process apoptotic process cell death programmed cell death positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to biotic stimulus immune response-activating signaling pathway innate immune response-activating signaling pathway response to other organism regulation of innate immune response response to external stimulus defense response to other organism positive regulation of defense response activation of innate immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway innate immune response response to external biotic stimulus nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway positive regulation of innate immune response nucleotide-binding oligomerization domain containing 1 signaling pathway defense response defense response to symbiont positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process multicellular organismal process cellular developmental process immature T cell proliferation in thymus cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte proliferation leukocyte activation T cell differentiation in thymus T cell activation cell differentiation lymphocyte proliferation anatomical structure development T cell differentiation T cell proliferation developmental process cell population proliferation hemopoiesis cell activation immature T cell proliferation mononuclear cell proliferation leukocyte differentiation positive regulation of response to cytokine stimulus regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus positive regulation of cytokine-mediated signaling pathway defense response to bacterium response to bacterium response to interleukin-12 catabolic process macroautophagy autophagy xenophagy metabolic process process utilizing autophagic mechanism interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-1 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process nucleotide-binding oligomerization domain containing 2 signaling pathway positive regulation of xenophagy regulation of autophagy positive regulation of macroautophagy positive regulation of autophagy regulation of xenophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy positive regulation of JNK cascade JNK cascade regulation of JNK cascade regulation of chemokine production chemokine production positive regulation of chemokine production cellular response to lipoteichoic acid response to oxygen-containing compound response to lipoteichoic acid cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to chemical stimulus response to molecule of bacterial origin positive regulation of cell population proliferation regulation of leukocyte activation regulation of alpha-beta T cell activation positive regulation of alpha-beta T cell proliferation regulation of cell activation positive regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of cell activation alpha-beta T cell proliferation positive regulation of leukocyte activation alpha-beta T cell activation regulation of leukocyte proliferation positive regulation of T cell activation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of alpha-beta T cell activation regulation of cell population proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of alpha-beta T cell proliferation positive regulation of lymphocyte activation positive regulation of CD4-positive, alpha-beta T cell activation cell adhesion cell-cell adhesion CD4-positive, alpha-beta T cell activation positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion regulation of lymphocyte proliferation CD4-positive, alpha-beta T cell proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation regulation of CD4-positive, alpha-beta T cell activation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of immune effector process positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response regulation of cytokine production involved in immune response immune effector process regulation of macrophage cytokine production positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of macrophage cytokine production macrophage cytokine production regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process protein K63-linked ubiquitination regulation of protein K63-linked ubiquitination positive regulation of protein modification process protein ubiquitination protein metabolic process protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein K63-linked ubiquitination positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process protein polyubiquitination primary metabolic process positive regulation of protein polyubiquitination macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of immature T cell proliferation positive regulation of immature T cell proliferation regulation of immature T cell proliferation in thymus positive regulation of immature T cell proliferation in thymus positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription interferon-alpha production regulation of interferon-alpha production positive regulation of type I interferon production type I interferon production positive regulation of interferon-alpha production regulation of type I interferon production positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction response to interleukin-18 immune response-regulating cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway cell surface toll-like receptor signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway cellular response to nitrogen compound cellular response to peptidoglycan response to nitrogen compound response to peptidoglycan positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production response to dsRNA response to exogenous dsRNA response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway response to lipopolysaccharide cellular response to lipid response to interleukin-1 positive regulation of T cell differentiation regulation of cell development multicellular organism development regulation of T-helper cell differentiation positive regulation of CD4-positive, alpha-beta T cell differentiation T-helper cell differentiation positive regulation of cell development regulation of T-helper 1 cell differentiation positive regulation of alpha-beta T cell differentiation regulation of developmental process CD4-positive, alpha-beta T cell differentiation positive regulation of T-helper cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation T cell activation involved in immune response positive regulation of cell differentiation leukocyte activation involved in immune response regulation of leukocyte differentiation regulation of cell differentiation cell activation involved in immune response positive regulation of T-helper 1 cell differentiation positive regulation of developmental process regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation alpha-beta T cell activation involved in immune response positive regulation of hemopoiesis lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development T cell differentiation involved in immune response T-helper 1 cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production toll-like receptor 2 signaling pathway regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production cellular response to muramyl dipeptide response to muramyl dipeptide regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production inflammatory response regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis regulation of type II interferon production type II interferon production positive regulation of type II interferon production defense response to Gram-positive bacterium positive regulation of phosphorylation regulation of protein phosphorylation peptidyl-tyrosine modification positive regulation of phosphate metabolic process positive regulation of peptidyl-tyrosine phosphorylation peptidyl-amino acid modification phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of peptidyl-tyrosine phosphorylation regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle membrane-bounded organelle vesicle cell periphery plasma membrane membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle membrane-bounded organelle vesicle cell periphery plasma membrane membrane protein-containing complex endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017322	Receptor-interacting serine/threonine-protein kinase 2	Family
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR042149	RIP2, CARD domain	Domain
A, B, C, D	IPR051681	Serine/Threonine Kinases and Pseudokinases	Family
A, B, C, D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR001315	CARD domain	Domain
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: O43353	ulcerative colitis renal cell carcinoma thyroid gland papillary carcinoma acute myeloid leukemia Carcinoma of thyroid gastric cancer hepatocellular carcinoma lung carcinoma thymic carcinoma astrocytic tumor Crohn disease gastric carcinoma invasive ductal breast carcinoma malignant ependymoma thyroid gland follicular carcinoma ulcerative colitis renal cell carcinoma thyroid gland papillary carcinoma acute myeloid leukemia Carcinoma of thyroid gastric cancer hepatocellular carcinoma lung carcinoma thymic carcinoma astrocytic tumor Crohn disease gastric carcinoma invasive ductal breast carcinoma malignant ependymoma thyroid gland follicular carcinoma chronic myelogenous leukemia, BCR-ABL1 positive endometrial carcinoma glioblastoma leprosy malignant mesothelioma

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.