3RZW | pdb_00003rzw

Crystal Structure of the Monobody ySMB-9 bound to human SUMO1

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	d3rzwb_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rzwa_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3rzwd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3rzwc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	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)
D	SCOP2B Superfamily	Ubiquitin-like	8043414	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8043414	3000157	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	DHDPS	e3rzwB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (v294.1)
A	Trypsin	e3rzwA1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: RIFT-related	T: Phage tail proteins	F: Trypsin	ECOD (v294.1)
D	DHDPS	e3rzwD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (v294.1)
C		e3rzwC1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: RIFT-related	T: Phage tail proteins	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF11976	Ubiquitin-2 like Rad60 SUMO-like (Rad60-SLD)	Ubiquitin-2 like Rad60 SUMO-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Monobody ySMB-9	-	-	-
C, 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR046332	Small ubiquitin-related modifier 1, Ubl domain	Domain
C, D	IPR000626	Ubiquitin-like domain	Domain
C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, D	IPR022617	Rad60/SUMO-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P63165	orofacial cleft 10 cleft palate Neoplasm Invasiveness cleft lip pancreatic intraductal papillary-mucinous neoplasm

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.