5XFP | pdb_00005xfp

Binary complex of PHF1 and a double stranded DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
E	GFP	e5xfpE2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: GFP	ECOD (v294.1)
E	Tudor_2	e5xfpE3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Tudor_2	ECOD (v294.1)
E	PF30898	e5xfpE5	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: PF30898	ECOD (v294.1)
B	GFP	e5xfpB2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: GFP	ECOD (v294.1)
B	Tudor_2	e5xfpB3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Tudor_2	ECOD (v294.1)
B	PF30898	e5xfpB5	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: PF30898	ECOD (v294.1)
A	GFP	e5xfpA4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: GFP	ECOD (v294.1)
A	Tudor_2	e5xfpA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Tudor_2	ECOD (v294.1)
A	PF30898	e5xfpA5	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: PF30898	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain
A, B, E	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
C, D	DNA (5'-D(GPGPGPCPGPGPCPCPGPCPCPCP*T)-3')	-	-	-
A, B, E	PHD finger protein 1	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding 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 DNA binding nucleic acid binding transcription factor binding transcription coregulator binding transcription corepressor binding protein binding 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 DNA binding nucleic acid binding histone methyltransferase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding histone H3K36me3 reader activity	cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus 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 negative regulation of biological process negative regulation of cellular process cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus 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 negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle protein-containing complex intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex nucleoplasm organelle lumen methyltransferase complex ESC/E(Z) complex nuclear lumen site of double-strand break site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.