3C6W | pdb_00003c6w

Crystal structure of the ING5 PHD finger in complex with H3K4me3 peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	PHD domain	8087156	4003778	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	FYVE/PHD zinc finger	8087157	3001459	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	FYVE/PHD zinc finger	8087157	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)
C	PHD_5	e3c6wC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
A	PHD_5	e3c6wA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	H3K4me3 histone peptide	-	-	-
A, C	Inhibitor of growth protein 5	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication cellular process apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular developmental process hemopoiesis cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation immune system process anatomical structure development regulation of hemopoiesis regulation of immune system process regulation of multicellular organismal process regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis chromatin organization DNA replication-dependent chromatin disassembly RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription fibroblast proliferation cell population proliferation protein acetylation macromolecule modification protein metabolic process protein modification process protein acylation negative regulation of cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process regulation of fibroblast proliferation negative regulation of fibroblast proliferation cell cycle regulation of cell cycle negative regulation of growth regulation of DNA biosynthetic process DNA biosynthetic process	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen MOZ/MORF histone acetyltransferase complex H3 histone acetyltransferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR001965	Zinc finger, PHD-type	Domain
A, C	IPR019787	Zinc finger, PHD-finger	Domain
A, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR028651	ING family	Family
A, C	IPR024610	Inhibitor of growth protein, N-terminal histone-binding	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q8WYH8	allergic rhinitis Crohn disease subependymal giant cell astrocytoma asthma oligodendroglioma tuberculosis brain glioma osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D	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.