5DV9 | pdb_00005dv9

Crystal structure of the Luciferase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5dv9a_	Multi-domain proteins (alpha and beta)	Acetyl-CoA synthetase-like	Acetyl-CoA synthetase-like	Acetyl-CoA synthetase-like	automated matches	Common eastern firefly (Photinus pyralis ) [TaxId: 7054 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	AMP-binding enzyme-like	8037622	3001902	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	AMP-binding enzyme C-terminal domain-like	8055417	3002292	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)
A	PPP2R1A-like_HEAT, VPS15-like_hel	e5dv9A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)
A	Phosphodiest, Metalloenzyme	e5dv9A4	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.38.10	Mainly Beta	Roll	Luciferase	domain 3	CATH (4.3.0)
A	3.40.50.980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Luciferin 4-monooxygenase	CoA-ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity acid-thiol ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding CoA-ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity acid-thiol ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity monooxygenase activity Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) oxidoreductase activity, acting on single donors with incorporation of molecular oxygen luciferin monooxygenase activity cation binding metal ion binding protein binding protein-folding chaperone binding	bioluminescence metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle peroxisome microbody cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020845	AMP-binding, conserved site	Conserved Site
A	IPR045851	AMP-binding enzyme domain superfamily	Homologous Superfamily
A	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
A	IPR000873	AMP-dependent synthetase/ligase 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.