5WCH | pdb_00005wch

Crystal structure of the catalytic domain of human USP9X

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	Cysteine proteinases	8081178	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8081178	3001808	SCOP2B (2022-06-29)
D	SCOP2 Family	USP domain-like	8081177	4003158	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Cysteine proteinases	8081178	3001808	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8081178	3001808	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	Pyr_redox_2	e5wchA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: Pyr_redox_2	ECOD (v294.1)
B	T6SS_VasJ	e5wchB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: T6SS_VasJ	ECOD (v294.1)
D	T6SS_VasJ	e5wchD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: T6SS_VasJ	ECOD (v294.1)
C	T6SS_VasJ	e5wchC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: T6SS_VasJ	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Probable ubiquitin carboxyl-terminal hydrolase FAF-X	co-SMAD binding SMAD binding protein binding binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity K11-linked deubiquitinase activity molecular sequestering activity K48-linked deubiquitinase activity co-SMAD binding SMAD binding protein binding binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity K11-linked deubiquitinase activity molecular sequestering activity K48-linked deubiquitinase activity cysteine-type endopeptidase activity endopeptidase activity K63-linked deubiquitinase activity cysteine-type deubiquitinase activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular process cell division cell cycle chromosome segregation cell cycle process primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular process cell division cell cycle chromosome segregation cell cycle process primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule 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 DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA alkylation repair cellular response to stress DNA damage response response to stress DNA repair cell migration cell motility catabolic process regulation of cellular process negative regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process regulation of biological process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process negative regulation of metabolic process proteasomal protein catabolic process protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of metabolic process regulation of protein catabolic process positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of TORC2 signaling regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of signaling regulation of TOR signaling regulation of TORC2 signaling positive regulation of intracellular signal transduction regulation of response to stimulus TORC2 signaling regulation of cell communication positive regulation of signaling cellular localization establishment of protein localization protein localization to peroxisome protein transmembrane import into intracellular organelle transport peroxisomal membrane transport cellular component organization localization peroxisome organization intercellular transport protein transmembrane transport establishment of localization in cell receptor metabolic process cellular component organization or biogenesis intracellular protein localization protein import into peroxisome matrix, receptor recycling establishment of protein localization to peroxisome intracellular protein transmembrane transport intracellular transport protein import into peroxisome matrix establishment of localization receptor recycling peroxisomal transport transmembrane transport organelle organization establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein transport axon extension multicellular organismal process axonogenesis cellular developmental process developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth nervous system development axon development cell morphogenesis involved in neuron differentiation developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development protein deubiquitination protein modification by small protein removal RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway cellular response to transforming growth factor beta stimulus response to endogenous stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway enzyme-linked receptor protein signaling pathway organelle assembly plasma membrane bounded cell projection assembly cytosolic ciliogenesis cellular component biogenesis cellular component assembly cilium assembly cilium organization cell projection assembly cellular response to BMP stimulus response to BMP BMP signaling pathway rhythmic process circadian rhythm regulation of circadian rhythm supramolecular fiber organization amyloid fibril formation monoubiquitinated protein deubiquitination protein K63-linked deubiquitination protein deubiquitination involved in ubiquitin-dependent protein catabolic process sexual reproduction reproductive process multicellular organismal reproductive process female gamete generation gamete generation neuron migration	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membraneless organelle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membraneless organelle cytoplasm cytosol centrosome microtubule organizing center microtubule cytoskeleton growth cone axon distal axon neuron projection site of polarized growth nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR055176	UBP24/USP9X/USP9Y, ubiquitin-like domain	Domain
A, B, C, D	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B, C, D	IPR056850	UBP34/UBP24/USP9X/USP9Y-like, ARM repeat region	Domain
A, B, C, D	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B, C, D	IPR021905	Ubiquitin C-terminal hydrolase-like, DUF3517	Domain
A, B, C, D	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
A, B, C, D	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q93008	intellectual disability, X-linked 99 intellectual disability choanal atresia MENTAL RETARDATION, X-LINKED 99, SYNDROMIC, FEMALE-RESTRICTED polydactyly glioblastoma intellectual disability, X-linked 99, syndromic, female-restricted non-syndromic X-linked intellectual disability ovarian cancer

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.