7LKY

Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641

External Resource: Annotation

Domain Annotation: ECOD Classification
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	PF18104	e7lkyA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
B	PF18104	e7lkyB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
C	PF18104	e7lkyC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
D	PF18104	e7lkyD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
E	PF18104	e7lkyE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
F	PF18104	e7lkyF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
G	PF18104	e7lkyG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18104	ECOD (1.6)
H	PF18104	e7lkyH1	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, G, H	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
A, B, C, D, E A, B, C, D, E, F, G, H	Isoform 1 of PHD finger protein 1	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding protein-containing complex binding chromatin binding DNA binding organic cyclic compound binding nucleic acid binding histone methyltransferase binding enzyme binding methylated histone binding modification-dependent protein binding transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding protein-containing complex binding chromatin binding DNA binding organic cyclic compound binding nucleic acid binding histone methyltransferase binding enzyme binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding cation binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus protein-containing complex organization protein-DNA complex organization cellular component organization cellular response to stress DNA damage response chromatin organization response to stress chromatin remodeling cellular process cellular component organization or biogenesis regulation of cellular process cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus protein-containing complex organization protein-DNA complex organization cellular component organization cellular response to stress DNA damage response chromatin organization response to stress chromatin remodeling cellular process cellular component organization or biogenesis 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 regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen site of double-strand break site of DNA damage chromosome
I [auth J], J [auth I], K, L, M, I [auth J], J [auth I], K, L, M, N, O, P	Peptidomimetic inhibitor UNC6641	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR025894	Polycomb-like MTF2 factor 2, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001965	Zinc finger, PHD-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002999	Tudor domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR047010	PHD finger protein 1, PHD finger 2	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019787	Zinc finger, PHD-finger	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR031202	PHD finger protein 1, PHD finger 1	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR047399	PHD finger protein 1, Tudor domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR040477	Lysine-specific demethylase 4-like, Tudor domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: O43189	attention deficit hyperactivity disorder, inattentive type large cell medulloblastoma osteosarcoma autism spectrum disorder lung cancer ovarian cancer endogenous depression malignant mesothelioma psoriasis

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 R01GM133198.