5HPT | pdb_00005hpt

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7

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	d5hpta_	Alpha and beta proteins (a+b)	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5hptd_	Alpha and beta proteins (a+b)	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5hptg_	Alpha and beta proteins (a+b)	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5hptb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5hpte_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5hpth_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5hptc_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5hptf_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	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)
A	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8036775	3000934	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8036775	3000934	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8036775	3000934	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBC-like	8034823	3000570	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	UBC-like	8034823	3000570	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	HECT	e5hptA1	A: a+b complex topology	X: Hect, E3 ligase catalytic domain (From Topology)	H: Hect, E3 ligase catalytic domain (From Topology)	T: Hect, E3 ligase catalytic domain	F: HECT	ECOD (1.6)
D	HECT	e5hptD1	A: a+b complex topology	X: Hect, E3 ligase catalytic domain (From Topology)	H: Hect, E3 ligase catalytic domain (From Topology)	T: Hect, E3 ligase catalytic domain	F: HECT	ECOD (1.6)
G	HECT	e5hptG1	A: a+b complex topology	X: Hect, E3 ligase catalytic domain (From Topology)	H: Hect, E3 ligase catalytic domain (From Topology)	T: Hect, E3 ligase catalytic domain	F: HECT	ECOD (1.6)
B	ubiquitin	e5hptB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)
E	ubiquitin	e5hptE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)
H	ubiquitin	e5hptH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)
C	UQ_con	e5hptC1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
F	UQ_con	e5hptF1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2160.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	CATH (utative)
A	3.30.2410.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic fold	Hect, E3 ligase catalytic domain	CATH (utative)
D	3.30.2160.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	CATH (utative)
D	3.30.2410.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic fold	Hect, E3 ligase catalytic domain	CATH (utative)
G	3.30.2160.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	CATH (utative)
G	3.30.2410.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic fold	Hect, E3 ligase catalytic domain	CATH (utative)
C	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
F	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G	PF00632	HECT-domain (ubiquitin-transferase) (HECT)	HECT-domain (ubiquitin-transferase)	The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.	Domain
B, E, H	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
C, F	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G	NEDD4-like E3 ubiquitin-protein ligase WWP1	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	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus response to stimulus signaling signal transduction cell communication catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol anchoring junction extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol anchoring junction cell junction cell periphery plasma membrane membrane protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular organelle nucleus intracellular membrane-bounded organelle
B, E, H	Ubiquitin variant P2.3	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal biosynthetic process cytoplasmic translation translation gene expression macromolecule biosynthetic process	membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
C, F	Ubiquitin-conjugating enzyme E2 L3	ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity enzyme regulator activity ubiquitin-protein transferase regulator activity molecular function activator activity ubiquitin-protein transferase activator activity enzyme activator activity ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity enzyme regulator activity ubiquitin-protein transferase regulator activity molecular function activator activity ubiquitin-protein transferase activator activity enzyme activator activity molecular function regulator activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding nucleic acid 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 ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cell cycle phase transition cell cycle cell cycle process regulation of cellular process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cell cycle phase transition cell cycle cell cycle process regulation of cellular process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process positive regulation of transferase activity regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cell population proliferation cellular response to stimulus response to lipid response to stimulus response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus cellular response to hormone stimulus protein localization regulation of localization establishment of protein localization cellular localization regulation of protein localization protein targeting regulation of protein targeting to mitochondrion positive regulation of establishment of protein localization localization cellular macromolecule localization positive regulation of protein targeting to mitochondrion regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting regulation of cellular localization macromolecule localization protein localization to organelle protein localization to mitochondrion positive regulation of protein localization protein targeting to mitochondrion establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein polyubiquitination RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription protein K11-linked ubiquitination response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus response to corticosteroid	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 ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G	IPR000569	HECT domain	Domain
A, D, G	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A, D, G	IPR024928	E3 ubiquitin-protein ligase, SMURF1 type	Family
A, D, G	IPR036020	WW domain superfamily	Homologous Superfamily
A, D, G	IPR000008	C2 domain	Domain
A, D, G	IPR035892	C2 domain superfamily	Homologous Superfamily
A, D, G	IPR001202	WW domain	Domain
A, D, G	IPR050409	E3 ubiquitin-protein ligase	Family
B, E, H	IPR019954	Ubiquitin conserved site	Conserved Site
B, E, H	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
B, E, H	IPR050158	Ubiquitin and ubiquitin-like	Family
B, E, H	IPR000626	Ubiquitin-like domain	Domain
B, E, H	IPR019956	Ubiquitin domain	Domain
B, E, H	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
B, E, H	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, F	IPR050113	Ubiquitin-conjugating enzyme	Family
C, F	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
C, F	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C, F	IPR000608	Ubiquitin-conjugating enzyme E2, catalytic core domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D, G	Pharos: Q9H0M0	Cowden disease osteosarcoma psoriasis Crohn disease ovarian cancer medulloblastoma Pick disease
B, E, H	Pharos: P62987	attention deficit hyperactivity disorder, inattentive type heart disease dental caries lung cancer gastroesophageal reflux disease plasma cell myeloma
C, F	Pharos: P68036	Crohn disease juvenile idiopathic arthritis chronic hepatitis B virus infection atypical teratoid rhabdoid tumor myositis psoriasis tuberculosis celiac disease hepatitis B virus infection lung cancer osteosarcoma systemic lupus erythematosus inflammatory bowel disease malignant mesothelioma ovarian cancer Crohn disease juvenile idiopathic arthritis chronic hepatitis B virus infection atypical teratoid rhabdoid tumor myositis psoriasis tuberculosis celiac disease hepatitis B virus infection lung cancer osteosarcoma systemic lupus erythematosus inflammatory bowel disease malignant mesothelioma ovarian cancer systemic sclerosis

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.