4NKG | pdb_00004nkg

Crystal structure of SspH1 LRR domain in complex PKN1 HR1b 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4nkgd_	All alpha proteins	Long alpha-hairpin	HR1 repeat	HR1 repeat	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4nkgb_	All alpha proteins	Long alpha-hairpin	HR1 repeat	HR1 repeat	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)
C	SCOP2B Superfamily	L domain-like	8096004	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L domain-like	8096004	3001010	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	OMPdecase	e4nkgD1	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: OMPdecase	ECOD (develop294)
B	EF-hand_1,S_100	e4nkgB1	A: alpha bundles	X: dsRBD-like	H: Peptidyl-tRNA hydrolase domain-like	T: Peptidyl-tRNA hydrolase domain-like	F: EF-hand_1,S_100	ECOD (develop294)
C	EF-hand_1,S_100	e4nkgC1	A: alpha bundles	X: dsRBD-like	H: Peptidyl-tRNA hydrolase domain-like	T: Peptidyl-tRNA hydrolase domain-like	F: EF-hand_1,S_100	ECOD (develop294)
A	EF-hand_1,S_100	e4nkgA1	A: alpha bundles	X: dsRBD-like	H: Peptidyl-tRNA hydrolase domain-like	T: Peptidyl-tRNA hydrolase domain-like	F: EF-hand_1,S_100	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.287.160	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	HR1 repeat	CATH (4.3.0)
B	1.10.287.160	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	HR1 repeat	CATH (4.3.0)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF02185	Hr1 repeat (HR1)	Hr1 repeat	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Serine/threonine-protein kinase N1	small GTPase binding protein binding binding enzyme binding GTPase binding histone binding histone deacetylase binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding small GTPase binding protein binding binding enzyme binding GTPase binding histone binding histone deacetylase 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 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 diacylglycerol-dependent serine/threonine kinase activity chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein serine kinase activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear androgen receptor binding histone H3 kinase activity histone modifying activity histone H3T11 kinase activity histone kinase activity kinase binding protein kinase C binding protein kinase binding	negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte activation negative regulation of mononuclear cell proliferation negative regulation of leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte activation negative regulation of mononuclear cell proliferation negative regulation of leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation negative regulation of cellular process regulation of immune system process regulation of multicellular organismal process negative regulation of B cell activation regulation of lymphocyte proliferation regulation of leukocyte proliferation regulation of biological process negative regulation of cell population proliferation cell population proliferation B cell activation biological regulation cell activation B cell proliferation negative regulation of B cell proliferation negative regulation of cell activation negative regulation of immune system process regulation of cell population proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation cellular process negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation renal system process system process B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis response to osmotic stress hyperosmotic response response to stimulus response to stress response to abiotic stimulus macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process developmental process immune system development multicellular organism development spleen development animal organ development anatomical structure development hematopoietic or lymphoid organ development system development protein phosphorylation phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process epithelium migration tissue migration ameboidal-type cell migration epithelial cell migration cell migration cell motility lymphocyte apoptotic process leukocyte apoptotic process B cell apoptotic process apoptotic process cell death programmed cell death cellular response to stimulus signaling signal transduction cell communication adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of developmental process regulation of germinal center formation immune response regulation of adaptive immune response adaptive immune response anatomical structure morphogenesis regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of response to stimulus anatomical structure formation involved in morphogenesis germinal center formation regulation of immune response regulation of anatomical structure morphogenesis regulation of biosynthetic process production of molecular mediator of immune response regulation of immune effector process immunoglobulin production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression regulation of immunoglobulin production biosynthetic process regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response regulation of metabolic process regulation of cell motility regulation of locomotion locomotion RNA metabolic process regulation of primary 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 nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription intracellular signal transduction intracellular receptor signaling pathway response to lipid regulation of signal transduction hormone-mediated signaling pathway cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway androgen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of signaling response to endogenous stimulus regulation of androgen receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid regulation of cell communication nuclear receptor-mediated signaling pathway	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol midbody cell division site cell periphery cleavage furrow membrane plasma membrane plasma membrane region membrane-bounded organelle nucleus membrane-enclosed lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol midbody cell division site cell periphery cleavage furrow membrane plasma membrane plasma membrane region membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle
A, C	E3 ubiquitin-protein ligase sspH1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity	primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal establishment of protein localization transport secretion primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal establishment of protein localization transport secretion protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport macromolecule localization intracellular protein localization	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle extracellular region host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR037317	Serine/threonine-protein kinase N1, second HR1 domain	Domain
B, D	IPR000719	Protein kinase domain	Domain
B, D	IPR017892	Protein kinase, C-terminal	Domain
B, D	IPR036274	HR1 repeat superfamily	Homologous Superfamily
B, D	IPR011072	HR1 rho-binding domain	Domain
B, D	IPR017441	Protein kinase, ATP binding site	Binding Site
B, D	IPR037784	Serine/threonine-protein kinase N, C2 domain	Domain
B, D	IPR000008	C2 domain	Domain
B, D	IPR000961	AGC-kinase, C-terminal	Domain
B, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B, D	IPR037313	Serine/threonine-protein kinase N, first HR1 domain	Domain
B, D	IPR035892	C2 domain superfamily	Homologous Superfamily
B, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A, C	IPR051071	Leucine-rich repeat-containing bacterial E3 ubiquitin ligases	Family
A, C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, C	IPR001611	Leucine-rich repeat	Repeat
A, C	IPR029487	Novel E3 ligase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q16512	acute myeloid leukemia colorectal adenocarcinoma Infiltrating duct carcinoma of female breast metastatic melanoma ovarian cancer aggressive systemic mastocytosis exocrine pancreatic carcinoma malignant glioma nephrolithiasis psoriasis atypical teratoid rhabdoid tumor glioblastoma mast cell leukemia osteosarcoma

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.