4E3C | pdb_00004e3c

X-ray crystal structure of human IKK2 in an active conformation

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	KOG4250	e4e3cF2	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: Inhibitor of kappaB kinase beta dimerization domain (From Topology)	T: Inhibitor of kappaB kinase beta dimerization domain	F: KOG4250	ECOD (1.6)
F	ubiquitin_4	e4e3cF3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
F	Pkinase_Tyr	e4e3cF1	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)
E	KOG4250	e4e3cE2	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: Inhibitor of kappaB kinase beta dimerization domain (From Topology)	T: Inhibitor of kappaB kinase beta dimerization domain	F: KOG4250	ECOD (1.6)
E	ubiquitin_4	e4e3cE3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
E	Pkinase_Tyr	e4e3cE1	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	KOG4250	e4e3cD2	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: Inhibitor of kappaB kinase beta dimerization domain (From Topology)	T: Inhibitor of kappaB kinase beta dimerization domain	F: KOG4250	ECOD (1.6)
D	ubiquitin_4	e4e3cD3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
D	Pkinase_Tyr	e4e3cD1	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	KOG4250	e4e3cC2	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: Inhibitor of kappaB kinase beta dimerization domain (From Topology)	T: Inhibitor of kappaB kinase beta dimerization domain	F: KOG4250	ECOD (1.6)
C	ubiquitin_4	e4e3cC3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
C	Pkinase_Tyr	e4e3cC1	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	KOG4250	e4e3cB3	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: Inhibitor of kappaB kinase beta dimerization domain (From Topology)	T: Inhibitor of kappaB kinase beta dimerization domain	F: KOG4250	ECOD (1.6)
B	ubiquitin_4	e4e3cB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
B	Pkinase_Tyr	e4e3cB1	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)
A	KOG4250	e4e3cA2	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: Inhibitor of kappaB kinase beta dimerization domain (From Topology)	T: Inhibitor of kappaB kinase beta dimerization domain	F: KOG4250	ECOD (1.6)
A	ubiquitin_4	e4e3cA3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
A	Pkinase_Tyr	e4e3cA1	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)
F	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F	1.20.1270.250	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
E	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E	1.20.1270.250	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	1.20.1270.250	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	1.20.1270.250	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	1.20.1270.250	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	1.20.1270.250	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF18397	IQBAL scaffold dimerization domain (IKBKB_SDD)	IQBAL scaffold dimerization domain	This is the C-terminal scaffold dimerization domain (SDD) found in inhibitor of nuclear factor kappa-B kinase subunit beta IKBKB (EC:2.7.11.10) [1]. IKK2 also known as IKBKB is one of the core component of IKB kinases (IKK). IKB kinase (IKK) is an en ...	This is the C-terminal scaffold dimerization domain (SDD) found in inhibitor of nuclear factor kappa-B kinase subunit beta IKBKB (EC:2.7.11.10) [1]. IKK2 also known as IKBKB is one of the core component of IKB kinases (IKK). IKB kinase (IKK) is an enzyme that quickly becomes active in response to diverse stresses on a cell. The SDD consists primarily of two long alpha-helices [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Inhibitor of nuclear factor kappa-B kinase subunit beta	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 IkappaB 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 identical protein binding protein binding protein heterodimerization activity protein dimerization activity transferrin receptor binding signaling receptor binding scaffold protein binding protein serine kinase activity protein homodimerization activity kinase binding enzyme binding protein kinase binding	regulation of biological process regulation of cellular process phosphorylation biological regulation phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process cellular process metabolic process phosphorus metabolic process regulation of metabolic process cellular response to stimulus regulation of defense response positive regulation of response to biotic stimulus regulation of biological process regulation of cellular process phosphorylation biological regulation phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process cellular process metabolic process phosphorus metabolic process regulation of metabolic process cellular response to stimulus regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus toll-like receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway MyD88-dependent toll-like receptor signaling pathway positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane regulation of signal transduction regulation of pattern recognition receptor signaling pathway regulation of toll-like receptor signaling pathway regulation of signaling regulation of cell communication positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process protein phosphorylation macromolecule modification protein metabolic process protein modification process signal transduction involved in regulation of gene expression immune response-regulating cell surface receptor signaling pathway cell surface receptor signaling pathway Fc receptor signaling pathway Fc-epsilon receptor signaling pathway peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus intracellular signal transduction cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway endolysosomal toll-like receptor signaling pathway toll-like receptor 3 signaling pathway positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of signaling immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway stress-activated MAPK cascade stress-activated protein kinase signaling cascade cellular response to stress MAPK cascade antigen processing and presentation antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of exogenous peptide antigen via MHC class I antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen bicellular tight junction assembly regulation of cellular component organization negative regulation of biological process tight junction organization cellular component organization cellular component biogenesis cellular component assembly negative regulation of cell junction assembly cell junction assembly negative regulation of cellular process cellular component organization or biogenesis cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly negative regulation of cellular component organization apical junction assembly regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization tight junction assembly negative regulation of bicellular tight junction assembly response to lectin cellular response to lectin innate immune response activating cell surface receptor signaling pathway stimulatory C-type lectin receptor signaling pathway TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway multicellular organismal process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process endothelium development cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development multicellular organism development cell differentiation regulation of endothelial cell development anatomical structure development regulation of multicellular organismal process developmental process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation tissue development epithelial cell development establishment of endothelial barrier protein maturation response to virus cellular response to interleukin-1 interleukin-1-mediated signaling pathway response to interleukin-1 inflammatory response regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production negative regulation of cytokine production involved in inflammatory response negative regulation of macromolecule metabolic process production of molecular mediator involved in inflammatory response negative regulation of metabolic process negative regulation of cytokine production cytokine production involved in inflammatory response negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex intracellular anatomical structure cytoplasm cytosol membrane microdomain cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex intracellular anatomical structure cytoplasm cytosol membrane microdomain membrane raft catalytic complex IkappaB kinase complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups serine/threonine protein kinase complex cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR051180	Inhibitor of nuclear factor kappa-B kinase	Family
A, B, C, D, E A, B, C, D, E, F	IPR000719	Protein kinase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046375	IKBKB, scaffold dimerization domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR022007	I-kappa-kinase-beta NEMO binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000626	Ubiquitin-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR041185	IKBKB, scaffold dimerization domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: O14920	severe combined immunodeficiency due to IKK2 deficiency hypertensive disorder severe combined immunodeficiency Hyperbilirubinemia, Neonatal psoriasis systemic lupus erythematosus astrocytic tumor Gaucher disease malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cancer glioblastoma osteosarcoma severe combined immunodeficiency due to IKK2 deficiency hypertensive disorder severe combined immunodeficiency Hyperbilirubinemia, Neonatal psoriasis systemic lupus erythematosus astrocytic tumor Gaucher disease malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cancer glioblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma lymphoplasmacytic lymphoma non-Hodgkin lymphoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm

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.