2PX9 | pdb_00002px9

The intrinsic affinity between E2 and the Cys domain of E1 in Ubiquitin-like modifications

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)
B	d2px9b_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	(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	SCCH domain-like	8003544	3000139	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)
B	RWD	e2px9B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	1.10.10.520	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin activating enzymes (Uba3). Chain: B, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	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
A	PF00899	ThiF family (ThiF)	ThiF family	This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	SUMO-conjugating enzyme UBC9	protein binding binding small protein activating enzyme binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO conjugating enzyme activity SUMO transferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity RING-like zinc finger domain binding protein binding binding small protein activating enzyme binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO conjugating enzyme activity SUMO transferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity RING-like zinc finger domain binding protein domain specific binding RNA binding nucleic acid binding transcription factor binding transcription coregulator 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 HLH domain binding	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 cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling macromolecule modification protein metabolic process protein modification process cell division cell cycle chromosome segregation cell cycle process peptidyl-lysine modification protein sumoylation peptidyl-amino acid modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal mitotic nuclear membrane reassembly membrane biogenesis mitotic cell cycle nuclear membrane reassembly cellular component organization cellular component biogenesis cellular component assembly cellular component organization or biogenesis endomembrane system organization membrane organization mitotic nuclear division organelle fission nuclear membrane organization membrane assembly nuclear division organelle organization nucleus organization mitotic cell cycle process mitotic nuclear membrane organization nuclear envelope organization catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport establishment of localization localization intercellular transport establishment of localization in cell nuclear export positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol presynapse presynaptic cytosol membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol presynapse presynaptic cytosol synapse cell junction protein-containing complex nuclear protein-containing complex nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen glutamatergic synapse catalytic complex SUMO ligase complex transferase complex condensed nuclear chromosome intracellular membraneless organelle nuclear chromosome chromosome membraneless organelle synaptonemal structure synaptonemal complex condensed chromosome Schaffer collateral - CA1 synapse perinuclear region of cytoplasm nuclear body PML body postsynapse postsynaptic cytosol
A	SUMO-activating enzyme subunit 2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ubiquitin-like modifier activating enzyme activity SUMO activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein catalytic activity ligase activity ATP-dependent activity protein binding small protein activating enzyme binding enzyme binding SUMO binding ubiquitin-like protein binding protein heterodimerization activity protein dimerization activity transferase activity ubiquitin-like protein conjugating enzyme binding	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm protein-containing complex catalytic complex SUMO activating enzyme complex nuclear protein-containing complex nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
B	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
B	IPR050113	Ubiquitin-conjugating enzyme E2-like	Family
A	IPR045886	ThiF/MoeB/HesA family	Family
A	IPR032426	SUMO-activating enzyme subunit 2, C-terminal domain	Domain
A	IPR042449	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	Homologous Superfamily
A	IPR030661	SUMO-activating enzyme subunit Uba2	Family
A	IPR000594	THIF-type NAD/FAD binding fold	Domain
A	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily
A	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
A	IPR028077	Ubiquitin/SUMO-activating enzyme ubiquitin-like domain	Domain
A	IPR023318	Ubiquitin activating enzyme, alpha domain superfamily	Homologous Superfamily
A	IPR018074	Ubiquitin-activating enzyme E1, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P63279	sarcomatoid carcinoma carcinoma Mammary Neoplasms, Experimental psoriasis undifferentiated carcinoma breast cancer glioblastoma lung cancer mammary neoplasms, animal non-small cell lung carcinoma pituitary cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma osteosarcoma plasma cell myeloma sarcomatoid carcinoma carcinoma Mammary Neoplasms, Experimental psoriasis undifferentiated carcinoma breast cancer glioblastoma lung cancer mammary neoplasms, animal non-small cell lung carcinoma pituitary cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma osteosarcoma plasma cell myeloma tuberculosis atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma ovarian cancer
A	Pharos: Q9UBT2	atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma

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.