2LV9 | pdb_00002lv9

Solution NMR structure of the PHD domain of human MLL5, Northeast structural genomics consortium target HR6512A

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PHD-1st_NSD	e2lv9A2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: PHD-1st_NSD	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	PF20826	PhD finger domain (PHD_5)	PhD finger domain	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	Histone-lysine N-methyltransferase MLL5	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity transcription coactivator activity transcription regulator activity transcription coregulator activity cation binding transition metal ion binding zinc ion binding ion binding binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity transcription coactivator activity transcription regulator activity transcription coregulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding protein binding enzyme binding	neutrophil mediated immunity immune system process leukocyte mediated immunity myeloid leukocyte mediated immunity immune effector process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization neutrophil mediated immunity immune system process leukocyte mediated immunity myeloid leukocyte mediated immunity immune effector process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process neutrophil activation multicellular organismal process cell activation myeloid leukocyte activation granulocyte activation leukocyte activation regulation of cell cycle phase transition positive regulation of biological process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process positive regulation of G1/S transition of mitotic cell cycle regulation of cell cycle process positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle G1/S phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle phase transition G1/S transition of mitotic cell cycle mitotic cell cycle phase transition 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process developmental process cellular developmental process homeostatic process hemopoiesis cell development erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation cell differentiation anatomical structure development homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton Rpd3L-Expanded complex protein-containing complex catalytic complex nuclear protein-containing complex nuclear chromosome chromosome chromatin histone deacetylase complex cell periphery plasma membrane membrane cytoplasm Set3 complex euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR001214	SET domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR044434	KMT2E, SET domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8IZD2	myeloid leukemia chronic monocytic leukemia Neurodevelopmental Disorders leukemia rheumatoid arthritis adenoma juvenile dermatomyositis medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia wet macular degeneration age-related macular degeneration Emery-Dreifuss muscular dystrophy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma myeloid leukemia chronic monocytic leukemia Neurodevelopmental Disorders leukemia rheumatoid arthritis adenoma juvenile dermatomyositis medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia wet macular degeneration age-related macular degeneration Emery-Dreifuss muscular dystrophy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma psoriasis autism spectrum disorder intellectual disability malignant pancreatic neoplasm myopathy ovarian cancer 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.