3KYD | pdb_00003kyd

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic

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)
C [auth D]	d3kydd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	SUMO-1 (smt3 homologue)	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)
C [auth D]	SCOP2B Superfamily	Ubiquitin-like	8043414	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003541	3000112	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003541	3000112	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	E2 binding domain-like	8003943	3000147	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003535	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003535	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003545	3000140	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)
C [auth D]	Pyr_redox	e3kydD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: HTH	T: winged helix domain	F: Pyr_redox	ECOD (v294.1)
B	RNase_T	e3kydB2	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (v294.1)
B	DctP	e3kydB1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: DctP	ECOD (v294.1)
A	Cupin_7	e3kydA2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Cupin_7	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	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)
B	3.10.290.20	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D]	PF11976	Ubiquitin-2 like Rad60 SUMO-like (Rad60-SLD)	Ubiquitin-2 like Rad60 SUMO-like	-	Family
B	PF14732	Ubiquitin/SUMO-activating enzyme ubiquitin-like domain (UAE_UbL)	Ubiquitin/SUMO-activating enzyme ubiquitin-like domain	This is the C-terminal domain of ubiquitin-activating enzyme and SUMO-activating enzyme 2. It is structurally similar to ubiquitin. This domain is involved in E1-SUMO-thioester transfer to the SUMO E2 conjugating protein [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	Small ubiquitin-related modifier 1	protein binding binding small protein activating enzyme binding enzyme binding RNA binding nucleic acid binding ubiquitin-specific protease binding protease binding ubiquitin-like protein ligase binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity protein tag activity protein binding binding small protein activating enzyme binding enzyme binding RNA binding nucleic acid binding ubiquitin-specific protease binding protease binding ubiquitin-like protein ligase binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity protein tag activity molecular tag activity potassium channel regulator activity channel regulator activity ion channel regulator activity ubiquitin protein ligase 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 negative regulation of transcription initiation by RNA polymerase II regulation of DNA-templated transcription initiation transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II negative regulation of DNA-templated transcription initiation heart process multicellular organismal process system process regulation of actin filament-based process regulation of heart contraction regulation of system process cardiac muscle contraction striated muscle contraction circulatory system process actin filament-based process regulation of multicellular organismal process blood circulation cardiac muscle cell contraction regulation of cardiac muscle contraction actin filament-based movement muscle contraction muscle system process regulation of muscle system process regulation of blood circulation regulation of striated muscle contraction regulation of actin filament-based movement regulation of muscle contraction regulation of cardiac muscle cell contraction actin-mediated cell contraction heart contraction negative regulation of protein transport regulation of localization establishment of protein localization cellular localization negative regulation of nucleocytoplasmic transport nucleocytoplasmic transport regulation of protein localization transport nuclear transport negative regulation of intracellular protein transport regulation of protein localization to nucleus negative regulation of transport negative regulation of protein import into nucleus localization import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus intracellular protein localization regulation of intracellular transport negative regulation of protein localization negative regulation of intracellular transport regulation of transport regulation of establishment of protein localization negative regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization negative regulation of protein localization to nucleus establishment of protein localization to organelle protein transport regulation of cellular localization macromolecule localization protein localization to organelle regulation of intracellular protein transport intracellular protein transport regulation of protein stability regulation of biological quality protein stabilization positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of biological process regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein localization to nuclear pore protein localization to nuclear envelope peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process nuclear body organization nucleus organization organelle organization PML body organization regulation of action potential negative regulation of action potential action potential regulation of membrane potential DNA metabolic process DNA damage response DNA repair cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to cadmium ion response to cadmium ion regulation of calcium ion transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport regulation of monoatomic ion transport transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport developmental process anatomical structure development roof of mouth development	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 nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol XY body sex chromosome chromosome presynapse presynaptic cytosol synapse cell junction cell periphery plasma membrane protein-containing complex nuclear protein-containing complex nuclear pore glutamatergic synapse nuclear stress granule PML body postsynapse postsynaptic cytosol
B	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
A	SUMO-activating enzyme subunit 1	protein binding binding ATP-dependent protein binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein ubiquitin activating enzyme activity catalytic activity ligase activity ATP-dependent activity protein binding binding ATP-dependent protein binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein ubiquitin activating enzyme activity catalytic activity ligase activity ATP-dependent activity small protein activating enzyme binding enzyme binding protein heterodimerization activity protein dimerization activity	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	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle protein-containing complex catalytic complex SUMO activating enzyme complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle membrane-enclosed lumen intracellular organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle protein-containing complex catalytic complex SUMO activating enzyme complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR046332	Small ubiquitin-related modifier 1, Ubl domain	Domain
C [auth D]	IPR000626	Ubiquitin-like domain	Domain
C [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C [auth D]	IPR022617	Rad60/SUMO-like domain	Domain
B	IPR045886	ThiF/MoeB/HesA family	Family
B	IPR032426	SUMO-activating enzyme subunit 2, C-terminal domain	Domain
B	IPR042449	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	Homologous Superfamily
B	IPR030661	SUMO-activating enzyme subunit Uba2	Family
B	IPR000594	THIF-type NAD/FAD binding fold	Domain
B	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily
B	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
B	IPR028077	Ubiquitin/SUMO-activating enzyme ubiquitin-like domain	Domain
B	IPR023318	Ubiquitin activating enzyme, alpha domain superfamily	Homologous Superfamily
B	IPR018074	Ubiquitin-activating enzyme E1, conserved site	Conserved Site
A	IPR000011	Ubiquitin/SUMO-activating enzyme E1-like	Family
A	IPR045886	ThiF/MoeB/HesA family	Family
A	IPR000594	THIF-type NAD/FAD binding fold	Domain
A	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D]	Pharos: P63165	orofacial cleft 10 cleft palate Neoplasm Invasiveness cleft lip pancreatic intraductal papillary-mucinous neoplasm
B	Pharos: Q9UBT2	atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma
A	Pharos: Q9UBE0	Adams-Oliver syndrome atypical teratoid rhabdoid tumor metabolic syndrome X rheumatoid arthritis adrenal cortex carcinoma lung cancer osteosarcoma astrocytic tumor medulloblastoma 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.