2LGG

Structure of PHD domain of UHRF1 in complex with H3 peptide

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FYVE/PHD zinc finger	8084742	3001459	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)
A	PHD_1	e2lggA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_1	ECOD (1.6)

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
B	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	E3 ubiquitin-protein ligase UHRF1	binding organic cyclic compound binding nucleic acid binding protein binding histone 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 binding organic cyclic compound binding nucleic acid binding protein binding histone 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding methylated histone binding modification-dependent protein binding H3K9me3 modified histone binding methylation-dependent protein binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding DNA damage sensor activity small molecule sensor activity hemi-methylated DNA-binding identical protein binding histone ubiquitin ligase activity histone H3 ubiquitin ligase activity histone modifying activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process organonitrogen compound metabolic process protein autoubiquitination primary metabolic process 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 nucleobase-containing compound metabolic process organic cyclic compound metabolic process homologous recombination DNA recombination DNA metabolic process nucleic acid metabolic process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of isomerase activity regulation of ATP-dependent activity regulation of catalytic activity positive regulation of ATP-dependent activity regulation of DNA topoisomerase (ATP-hydrolyzing) activity positive regulation of catalytic activity regulation of molecular function positive regulation of molecular function positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity positive regulation of isomerase activity positive regulation of protein metabolic process regulation of protein metabolic process cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation double-strand break repair recombinational repair double-strand break repair via homologous recombination DNA repair heterochromatin formation non-membrane-bounded organelle assembly microtubule cytoskeleton organization mitotic cell cycle cellular component biogenesis cellular component assembly mitotic sister chromatid segregation cell cycle chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle assembly organelle fission chromosome organization sister chromatid segregation spindle assembly mitotic spindle organization mitotic spindle assembly organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization	intracellular organelle protein-containing complex intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle heterochromatin cytoskeleton spindle microtubule cytoskeleton intracellular organelle protein-containing complex intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle heterochromatin cytoskeleton spindle microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nuclear matrix nucleoplasm replication fork euchromatin
B	histone H3 peptide	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015947	PUA-like superfamily	Homologous Superfamily
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR047406	E3 ubiquitin-protein ligase UHRF1, ubiquitin-like domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR001841	Zinc finger, RING-type	Domain
A	IPR036987	SRA-YDG superfamily	Homologous Superfamily
A	IPR003105	SRA-YDG	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR021991	UHRF1, tandem tudor domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR045134	UHRF1/2-like	Family
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR007125	Histone H2A/H2B/H3	Domain
B	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96T88	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis skin basal cell carcinoma atopic eczema breast cancer endometriosis hypothyroidism large cell medulloblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer adenoid cystic carcinoma salivary gland adenoid cystic carcinoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis skin basal cell carcinoma atopic eczema breast cancer endometriosis hypothyroidism large cell medulloblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma tuberculosis adrenal cortex carcinoma attention deficit hyperactivity disorder, inattentive type breast carcinoma glioblastoma interstitial cystitis lung adenocarcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor Sjogren syndrome vitiligo astrocytic tumor atypical teratoid rhabdoid tumor ductal breast carcinoma in situ hepatocellular carcinoma invasive ductal breast carcinoma malignant ependymoma
B	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.