3U9M | pdb_00003u9m

Structure of reduced human FBXL5 hemerythrin like domain

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)
D [auth G]	Hemerythrin_1	e3u9mG1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Hemerythrin (From Topology)	T: Hemerythrin	F: Hemerythrin_1	ECOD (1.6)
C [auth E]	Hemerythrin_1	e3u9mE1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Hemerythrin (From Topology)	T: Hemerythrin	F: Hemerythrin_1	ECOD (1.6)
B [auth C]	Hemerythrin_1	e3u9mC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Hemerythrin (From Topology)	T: Hemerythrin	F: Hemerythrin_1	ECOD (1.6)
A	Hemerythrin_1	e3u9mA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Hemerythrin (From Topology)	T: Hemerythrin	F: Hemerythrin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth G]	1.20.120.520	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	nmb1532 protein domain like	CATH (4.3.0)
C [auth E]	1.20.120.520	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	nmb1532 protein domain like	CATH (4.3.0)
B [auth C]	1.20.120.520	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	nmb1532 protein domain like	CATH (4.3.0)
A	1.20.120.520	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	nmb1532 protein domain like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G]	PF01814	Hemerythrin HHE cation binding domain (Hemerythrin)	Hemerythrin HHE cation binding domain	Iteration of the HHE family ([2]) found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain ([1]) in fact consists of two cation binding domains. Members of this family occur all across nature and are ...	Iteration of the HHE family ([2]) found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain ([1]) in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor Swiss:P80255 binds Cadmium so as to protect the organism from toxicity ([3]). However Hemerythrin is classically described as Oxygen-binding through two attached Fe2+ ions. And the bacterial Swiss:Q7WX96 is a regulator of response to NO, which suggests yet another set-up for its metal ligands ([4]). In Staphylococcus aureus P72360 has been noted to be important when the organism switches to living in environments with low oxygen concentrations ([4]); perhaps this protein acts as an oxygen store or scavenger. This domain can bind oxygen (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043)	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E], D [auth G]	F-box/LRR-repeat protein 5	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis multicellular organismal-level iron ion homeostasis multicellular organismal process multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis multicellular organismal-level iron ion homeostasis multicellular organismal process multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal proteolysis involved in protein catabolic process proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G]	IPR036047	F-box-like domain superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR001611	Leucine-rich repeat	Repeat
A, B [auth C], C [auth E], D [auth G]	IPR001810	F-box domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR045808	FBXL5-like, hemerythrin-like domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR012312	Hemerythrin-like	Domain
A, B [auth C], C [auth E], D [auth G]	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], C [auth E], D [auth G]	Pharos: Q9UKA1	cystic fibrosis lung cancer ovarian cancer tuberculosis invasive ductal breast carcinoma lymphoplasmacytic lymphoma plasma cell myeloma large cell medulloblastoma 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.