6WAU | pdb_00006wau

Complex structure of PHF19

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Pro_isomerase	e6wauF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
E	Pro_isomerase	e6wauE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
D	Pro_isomerase	e6wauD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
C	Pro_isomerase	e6wauC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
B	Pro_isomerase	e6wauB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
A	Pro_isomerase	e6wauA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF18104	Jumonji domain-containing protein 2A Tudor domain (Tudor_2)	Jumonji domain-containing protein 2A Tudor domain	This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means o ...	This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms [3]. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD) [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	Histone H3.1t peptide	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 heterochromatin organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 heterochromatin organization developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process spermatogonial cell division developmental process involved in reproduction male gamete generation gamete generation cell division DNA replication-dependent chromatin assembly regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process cell differentiation biological regulation regulation of cell differentiation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex protein-DNA complex nucleosome chromosome, telomeric region chromosomal region nucleoplasm
A, B, C, D, E A, B, C, D, E, F	PHD finger protein 19	DNA binding binding nucleic acid binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding cation binding transition metal ion binding zinc ion binding ion binding DNA binding binding nucleic acid binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K36me3 reader activity	developmental process multicellular organismal process maintenance of cell number stem cell population maintenance 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 developmental process multicellular organismal process maintenance of cell number stem cell population maintenance 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II 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 stem cell differentiation cellular developmental process cell differentiation 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	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex intracellular organelle cellular anatomical structure membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex ESC/E(Z) complex nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, J, K G, H, I, J, K, L	IPR009072	Histone-fold	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR000164	Histone H3/CENP-A	Family
A, B, C, D, E A, B, C, D, E, F	IPR047400	PHD finger protein 19, Tudor domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR025894	Polycomb-like MTF2 factor 2, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001965	Zinc finger, PHD-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002999	Tudor domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR019787	Zinc finger, PHD-finger	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR042017	PHF19, PHD domain 2	Domain
A, B, C, D, E A, B, C, D, E, F	IPR040477	Lysine-specific demethylase 4-like, Tudor domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G, H, I, J, K G, H, I, J, K, L	Pharos: Q16695	intellectual disability bagassosis pneumoconiosis Mental deficiency breast carcinoma
A, B, C, D, E A, B, C, D, E, F	Pharos: Q5T6S3	rheumatoid arthritis allergic rhinitis lung adenocarcinoma non-small cell lung carcinoma psoriasis breast cancer malignant glioma osteosarcoma glioblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K G, H, I, J, K, L	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.