6BG3 | pdb_00006bg3

Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl acetate bound to DCN1

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055670	3001983	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055669	3001983	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)
A		e6bg3A1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Amidohydro_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (utative)
A	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A	PF03556	Cullin binding (Cullin_binding)	Cullin binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Endolysin, DCN1-like protein 1 chimera	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity protein binding binding ubiquitin-like protein binding ubiquitin-like protein conjugating enzyme binding enzyme binding ubiquitin conjugating enzyme binding cullin family protein binding	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process regulation of biological process regulation of cellular process regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of protein ubiquitination primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process protein ubiquitination macromolecule modification protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein neddylation regulation of protein neddylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein neddylation	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part 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 ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR052619	Bacteriophage lysozyme-like	Family
A	IPR001165	T4-type lysozyme	Family
A	IPR034690	Endolysin T4 type	Family
A	IPR002196	Glycoside hydrolase, family 24	Family
A	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A	IPR042460	DCN1-like, PONY binding domain	Homologous Superfamily
A	IPR009060	UBA-like superfamily	Homologous Superfamily
A	IPR005176	Potentiating neddylation domain	Domain
A	IPR014764	Defective-in-cullin neddylation protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96GG9	breast cancer malignant mesothelioma osteosarcoma pituitary cancer sarcoidosis cancer myopathy ovarian cancer prostate carcinoma tuberculosis large cell medulloblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis

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.