5XVW | pdb_00005xvw

Crystal structure of AL2 PAL domain in complex with AtRing1a distal site

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	HNH	e5xvwE1	A: a/b three-layered sandwiches	X: HUP domain-like	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH	ECOD (v294.1)
D [auth C]	HNH	e5xvwC1	A: a/b three-layered sandwiches	X: HUP domain-like	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH	ECOD (v294.1)
B	HNH	e5xvwB1	A: a/b three-layered sandwiches	X: HUP domain-like	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH	ECOD (v294.1)
A	Alfin	e5xvwA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Alfin	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D [auth C], E	PF12165	Alfin (Alfin)	Alfin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], F	AtRing1a distal binding site	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity	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 developmental process cellular developmental process cell differentiation cell fate determination cell fate commitment multicellular organismal process meristem development meristem maintenance maintenance of inflorescence meristem identity anatomical structure development maintenance of cell number tissue development maintenance of meristem identity stem cell population maintenance protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal maintenance of floral meristem identity maintenance of shoot apical meristem identity multicellular organism development post-embryonic development seed germination seedling development cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic plant organ development root development system development root system development	membrane-bounded organelle protein-containing complex PRC1 complex intracellular anatomical structure ubiquitin ligase complex catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure nuclear ubiquitin ligase complex membrane-bounded organelle protein-containing complex PRC1 complex intracellular anatomical structure ubiquitin ligase complex catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure nuclear ubiquitin ligase complex organelle intracellular protein-containing complex
A, B, D [auth C], E	PHD finger protein ALFIN-LIKE 2	protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity transcription coregulator activity cation binding transition metal ion binding protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity transcription coregulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], F	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C [auth D], F	IPR044592	Putative E3 ubiquitin-protein ligase RING1a/b	Family
C [auth D], F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C [auth D], F	IPR001841	Zinc finger, RING-type	Domain
A, B, D [auth C], E	IPR001965	Zinc finger, PHD-type	Domain
A, B, D [auth C], E	IPR045104	Alfin	Family
A, B, D [auth C], E	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, D [auth C], E	IPR019787	Zinc finger, PHD-finger	Domain
A, B, D [auth C], E	IPR044104	Alfin1-like, PHD finger	Domain
A, B, D [auth C], E	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, D [auth C], E	IPR021998	Alfin, N-terminal	Domain
A, B, D [auth C], E	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.