4NHY | pdb_00004nhy

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Clavaminate synthase-like	8089985	3001848	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Clavaminate synthase-like	8089985	3001848	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Clavaminate synthase-like	8089985	3001848	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clavaminate synthase-like	8089985	3001848	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)
D	Ofd1_CTDD	e4nhyD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Ofd1_CTDD	ECOD (1.6)
D	2OG-FeII_Oxy_3	e4nhyD2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)
C	Ofd1_CTDD	e4nhyC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Ofd1_CTDD	ECOD (1.6)
C	2OG-FeII_Oxy_3	e4nhyC2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)
B	Ofd1_CTDD	e4nhyB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Ofd1_CTDD	ECOD (1.6)
B	2OG-FeII_Oxy_3	e4nhyB2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)
A	Ofd1_CTDD	e4nhyA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Ofd1_CTDD	ECOD (1.6)
A	2OG-FeII_Oxy_3	e4nhyA2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
C	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
B	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13661	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_4)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1].	Domain
A, B, C, D	PF10637	Oxoglutarate and iron-dependent oxygenase degradation C-term (Ofd1_CTDD)	Oxoglutarate and iron-dependent oxygenase degradation C-term	Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory ele ...	Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline 3-dioxygenase activity peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline 3-dioxygenase activity peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding carbohydrate binding vitamin binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding	primary metabolic process macromolecule modification peptidyl-proline hydroxylation peptidyl-amino acid modification protein hydroxylation peptidyl-proline modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process cellular component biogenesis cellular component organization organelle organization primary metabolic process macromolecule modification peptidyl-proline hydroxylation peptidyl-amino acid modification protein hydroxylation peptidyl-proline modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process cellular component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis cell population proliferation regulation of cellular process regulation of cellular component organization protein-containing complex disassembly protein biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process post-transcriptional regulation of gene expression translational termination regulation of biosynthetic process cellular component disassembly regulation of biological process protein-containing complex organization regulation of protein metabolic process regulation of translational termination biological regulation regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol membrane-bounded organelle nucleus intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, B, C, D	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, B, C, D	IPR051842	Ribosomal subunit uS12 prolyl hydroxylase	Family
A, B, C, D	IPR039558	Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain	Domain
A, B, C, D	IPR019601	Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q8N543	breast cancer pancreatic ductal adenocarcinoma tuberculosis osteosarcoma psoriasis ovarian cancer subependymal giant cell astrocytoma

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.