3DKM | pdb_00003dkm

Crystal structure of the HECTD1 CPH 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)
A	d3dkma1	All beta proteins	SH3-like barrel	Mib/herc2 domain-like	Mib/herc2 domain	E3 ubiquitin-protein ligase hectd1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3dkma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	Mib/herc2 domain-like	8033772	3000237	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	MIB_HERC2	e3dkmA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MIB_HERC2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF06701	Mib_herc2 (MIB_HERC2)	Mib_herc2	Named "mib/herc2 domain" in [1]. Usually the protein also contains an E3 ligase domain (either Ring or Hect).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	E3 ubiquitin-protein ligase HECTD1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding ion binding binding metal ion binding small molecule binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process developmental process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process developmental process heart development multicellular organismal process animal organ development ventricular septum development circulatory system development multicellular organism development cardiac septum development cardiac chamber development anatomical structure development cardiac ventricle development system development heart valve development positive regulation of proteasomal protein catabolic process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation proteasomal protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of metabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal artery development aorta development vasculature development blood vessel development	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002110	Ankyrin repeat	Repeat
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR000569	HECT domain	Domain
A	IPR012919	SUN domain	Domain
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR037252	Mib/herc2 domain superfamily	Homologous Superfamily
A	IPR010606	Mib-herc2	Domain
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR045322	E3 ubiquitin-protein ligase HECTD1/TRIP12-like	Family
A	IPR041200	FKBP3, basic tilted helix bundle domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9ULT8	astrocytic tumor Duchenne muscular dystrophy malignant ependymoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis Becker muscular dystrophy Emery-Dreifuss muscular dystrophy malignant glioma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida chronic obstructive pulmonary disease astrocytic tumor Duchenne muscular dystrophy malignant ependymoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis Becker muscular dystrophy Emery-Dreifuss muscular dystrophy malignant glioma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida chronic obstructive pulmonary disease head and neck cancer malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease

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.