6YDV

Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth AAA]	JmjC_1	e6ydvAAA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC_1	ECOD (1.6)
B [auth BBB]	JmjC_1	e6ydvBBB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], B [auth BBB]	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAA], B [auth BBB]	JMJD1B protein	catalytic activity, acting on a protein protein demethylase activity histone H3K9 demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity catalytic activity demethylase activity DNA binding binding chromatin binding organic cyclic compound binding nucleic acid binding chromatin DNA binding catalytic activity, acting on a protein protein demethylase activity histone H3K9 demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity catalytic activity demethylase activity DNA binding binding chromatin binding organic cyclic compound binding nucleic acid binding chromatin DNA binding cation binding ion binding metal ion binding small molecule binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II 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 regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process demethylation	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], B [auth BBB]	IPR045109	Histone demethylase JHDM2-like	Family
A [auth AAA], B [auth BBB]	IPR003347	JmjC domain	Domain

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.