6WAU

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)
A	PF18104	e6wauA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
C	PF18104	e6wauC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
D	PF18104	e6wauD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
E	PF18104	e6wauE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
B	PF18104	e6wauB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
F	PF18104	e6wauF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)

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
G, H, I, J, K G, H, I, J, K, L	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, B, C, D, E A, B, C, D, E, F	PHD finger protein 19	DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding methylated histone binding protein binding modification-dependent protein binding histone binding methylation-dependent protein binding cation binding ion binding metal ion binding DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding methylated histone binding protein binding modification-dependent protein binding histone binding methylation-dependent protein binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process developmental process multicellular organismal process maintenance of cell number stem cell population maintenance negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative 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 negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process stem cell differentiation cellular developmental process cell differentiation protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis protein-containing complex organization 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 cellular anatomical entity transferase complex intracellular organelle lumen PcG protein complex intracellular organelle 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 cellular anatomical entity transferase complex intracellular organelle lumen PcG protein complex intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex ESC/E(Z) complex nuclear lumen
G, H, I, J, K G, H, I, J, K, L	Histone H3.1t peptide	DNA binding binding organic cyclic compound 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 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	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity 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 chromosome, telomeric region chromosomal region 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, 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
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	Histone H2A/H2B/H3	Domain
G, H, I, J, K G, H, I, J, K, L	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
G, H, I, J, K G, H, I, J, K, L	Pharos: Q16695	intellectual disability bagassosis pneumoconiosis Mental deficiency breast carcinoma

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 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.