2PNX | pdb_00002pnx

The PHD finger of ING4 in complex with an H3K4Me3 histone peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d2pnxc1	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	Inhibitor of growth protein 4, Ing4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2pnxa1	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	Inhibitor of growth protein 4, Ing4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	FYVE/PHD zinc finger	8035875	3001459	SCOP2B (2022-06-29)
A	SCOP2 Family	PHD domain	8023495	4003778	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FYVE/PHD zinc finger	8035875	3001459	SCOP2 (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	Ribosomal_S14	e2pnxC1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Ribosomal_S14	ECOD (v294.1)
A	PHD	e2pnxA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)

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
A, C	Inhibitor of growth protein 4	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	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 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 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 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 negative regulation of DNA-templated transcription regulation of biological process 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 cell cycle G2/M phase transition regulation of cell cycle phase transition regulation of cell cycle process regulation of cell cycle G2/M phase transition cell cycle phase transition cell cycle regulation of cell cycle cell cycle process apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular 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 cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication positive regulation of response to stimulus cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator regulation of signaling positive regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of intracellular signal transduction signal transduction by p53 class mediator regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage positive regulation of signaling protein acetylation macromolecule modification protein metabolic process protein modification process protein acylation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of growth regulation of DNA biosynthetic process DNA metabolic process DNA biosynthetic process regulation of DNA metabolic process chromatin remodeling	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 cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cytoskeleton intermediate filament cytoskeleton
B, D	H3K4Me3 peptide	-	-	-

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: Q9UNL4	colorectal cancer Lymphatic Metastasis cancer colorectal carcinoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.