2LVA | pdb_00002lva

NMR solution structure of the N-terminal domain of human USP28, Northeast structural genomics consortium target HT8470A

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)
A	Pkinase, Kdo	e2lvaA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Pkinase, Kdo	ECOD (v294.1)
A	CBS	e2lvaA3	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	6.10.250.1720	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21909	Ubiquitin-specific protease UIM domain (USP_UIM_N)	Ubiquitin-specific protease UIM domain	This entry represents the N-terminal ubiquitin-interacting motif (UIM) found in a number of ubiquitin-specific proteases (USP) [1]. This domain provides a structural basis for the recognition and recruitment of ubiquitin substrates, potentially confe ...	This entry represents the N-terminal ubiquitin-interacting motif (UIM) found in a number of ubiquitin-specific proteases (USP) [1]. This domain provides a structural basis for the recognition and recruitment of ubiquitin substrates, potentially conferring USP display of catalytic activity [2].	Domain
A	PF22566	UBA-like domain (UBA_8)	UBA-like domain	This entry represents a UBA-like domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin carboxyl-terminal hydrolase 28	ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell population proliferation protein deubiquitination catabolic process primary metabolic process protein catabolic process protein deubiquitination involved in ubiquitin-dependent protein catabolic process macromolecule catabolic process protein modification by small protein removal cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell population proliferation protein deubiquitination catabolic process primary metabolic process protein catabolic process protein deubiquitination involved in ubiquitin-dependent protein catabolic process macromolecule catabolic process protein modification by small protein removal modification-dependent macromolecule catabolic process modification-dependent protein catabolic process macromolecule modification metabolic process ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal response to ionizing radiation response to radiation response to abiotic stimulus regulation of protein stability biological regulation regulation of biological quality response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair regulation of biological process regulation of cellular process signaling signal transduction by p53 class mediator cell death intracellular signal transduction intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of biological process negative regulation of cell cycle cell cycle phase transition negative regulation of cellular process negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol 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 intracellular membraneless organelle nuclear body membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR054108	Ubiquitin carboxyl-terminal hydrolase 25/28, UIM	Conserved Site
A	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR054109	UBA-like domain	Domain
A	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
A	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A	IPR009060	UBA-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96RU2	prostate cancer attention deficit hyperactivity disorder, inattentive type osteosarcoma prostate carcinoma large cell medulloblastoma ovarian cancer Prostatic Neoplasms non-small cell lung carcinoma

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.