2RSD | pdb_00002rsd

Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2rsda1	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	automated matches	automated matches	Japanese rice (Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)
A	d2rsda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Japanese rice (Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PHD domain	8086398	4003778	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FYVE/PHD zinc finger	8086399	3001459	SCOP2 (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	Peptidase_M27	e2rsdA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: Peptidase_M27	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	E3 SUMO-protein ligase SIZ1	aminoacyltransferase activity ubiquitin-like protein transferase activity SUMO ligase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity SUMO transferase activity transferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity SUMO ligase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity SUMO transferase activity transferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR004181	Zinc finger, MIZ-type	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR003034	SAP domain	Domain
A	IPR036361	SAP domain superfamily	Homologous Superfamily
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR031141	E3 SUMO-protein ligase SIZ1/2, SP-RING finger	Domain
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

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.