3U21 | pdb_00003u21

Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8092001	3000034	SCOP2B (2022-06-29)
A	SCOP2 Family	NFRKB WHD-like	8050026	4006730	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8092001	3000034	SCOP2 (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	Pkinase, APH	e3u21B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)
A	HIT	e3u21A1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: HIT-related	T: HIT-related	F: HIT	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.2430	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	NFRKB winged helix-like domain	CATH (4.3.0)
A	1.10.10.2430	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	NFRKB winged helix-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14465	NFRKB Winged Helix-like (WHD_1st_NFRKB)	NFRKB Winged Helix-like	This domain covers regions 370-495 of human nuclear factor related to kappaB binding (NFRKB) protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Nuclear factor related to kappa-B-binding protein	DNA binding binding nucleic acid binding protein binding enzyme binding protease binding	regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation chromosome organization regulation of chromosome organization regulation of organelle organization cellular component organization organelle organization cellular process cellular component organization or biogenesis cellular response to stimulus response to stimulus primary metabolic process regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation chromosome organization regulation of chromosome organization regulation of organelle organization cellular component organization organelle organization cellular process cellular component organization or biogenesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process DNA replication regulation of DNA replication regulation of DNA metabolic process developmental process multicellular organismal process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development regulation of multicellular organismal process cell cycle regulation of cell cycle positive regulation of organelle organization regulation of telomere maintenance telomere maintenance in response to DNA damage positive regulation of cellular component organization regulation of cellular response to stress telomere organization positive regulation of response to stimulus regulation of response to stress positive regulation of telomere maintenance in response to DNA damage positive regulation of telomere maintenance regulation of telomere maintenance in response to DNA damage positive regulation of chromosome organization telomere maintenance positive regulation of DNA metabolic process regulation of response to stimulus regulation of DNA repair regulation of DNA strand elongation DNA strand elongation positive regulation of DNA repair DNA recombination chromatin organization chromatin remodeling	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle SWI/SNF superfamily-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle SWI/SNF superfamily-type complex INO80-type complex catalytic complex intracellular membraneless organelle chromatin intracellular membrane-bounded organelle Ino80 complex organelle lumen organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR057748	Nuclear factor related to kappa-B-binding protein, second winged helix domain	Domain
A, B	IPR044867	DEUBAD domain	Domain
A, B	IPR025220	Nuclear factor related to kappa-B-binding protein, winged helix-like domain	Domain
A, B	IPR038106	NFRKB winged helix-like domain superfamily	Homologous Superfamily
A, B	IPR024867	Nuclear factor related to kappa-B-binding protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q6P4R8	lung cancer osteosarcoma malignant ependymoma psoriasis malignant mesothelioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084
A, B	MSE	Parent Component: MET RESID: AA0075

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.