4MLP | pdb_00004mlp

Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
D	d4mlpd2	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d4mlpd1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth B]	d4mlpb2	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth B]	d4mlpb1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d4mlpa2	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d4mlpa1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth C]	d4mlpc2	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth C]	d4mlpc1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	DcpS_C	e4mlpD3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (develop294)
C [auth B]	DcpS_C	e4mlpB3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (develop294)
B [auth A]	DcpS_C	e4mlpA3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (develop294)
A [auth C]	DcpS_C	e4mlpC3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
C [auth B]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C [auth B]	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C [auth B]	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
B [auth A]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B [auth A]	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B [auth A]	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
A [auth C]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A [auth C]	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A [auth C]	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth B], D	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
A [auth C], B [auth A], C [auth B], D	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth A], C [auth B], D	Cryptochrome-2	enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding damaged DNA binding protein binding kinase binding enzyme binding protein kinase binding phosphatase binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding molecular transducer activity photoreceptor activity signaling receptor activity single-stranded DNA binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process multicellular organismal process regulation of localization system process regulation of system process negative regulation of transport negative regulation of lipid localization cell communication regulation of glucocorticoid secretion localization regulation of steroid hormone secretion negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality negative regulation of steroid hormone secretion regulation of hormone levels lipid transport regulation of corticosteroid hormone secretion establishment of localization regulation of secretion endocrine hormone secretion lipid export from cell negative regulation of corticosteroid hormone secretion glucocorticoid secretion negative regulation of multicellular organismal process regulation of endocrine process corticosteroid hormone secretion regulation of hormone secretion transport signaling negative regulation of signaling steroid hormone secretion regulation of lipid transport hormone secretion negative regulation of cell communication secretion by cell regulation of secretion by cell signal release regulation of multicellular organismal process negative regulation of glucocorticoid secretion regulation of signaling negative regulation of lipid transport secretion regulation of transport lipid localization export from cell cell-cell signaling endocrine process regulation of lipid localization macromolecule localization hormone transport regulation of cell communication rhythmic process circadian rhythm regulation of circadian rhythm response to stimulus response to activity response to light stimulus response to radiation response to abiotic stimulus sodium-dependent phosphate transport regulation of phosphate transport regulation of sodium-dependent phosphate transport phosphate ion transport inorganic anion transport establishment of protein localization cellular localization nucleocytoplasmic transport nuclear transport intracellular transport protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport negative regulation of circadian rhythm cellular response to stimulus intracellular receptor signaling pathway response to lipid negative regulation of intracellular signal transduction regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus negative regulation of intracellular steroid hormone receptor signaling pathway response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus negative regulation of response to stimulus response to endogenous stimulus nuclear receptor-mediated corticosteroid signaling pathway negative regulation of signal transduction cellular response to chemical stimulus regulation of response to stimulus response to chemical cellular response to lipid negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated signaling pathway regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway circadian regulation of gene expression entrainment of circadian clock response to external stimulus photoperiodism entrainment of circadian clock by photoperiod response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound lipid storage nutrient storage transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex Cry-Per complex transcription repressor complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex Cry-Per complex transcription repressor complex membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytosol extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth A], C [auth B], D	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A [auth C], B [auth A], C [auth B], D	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth B], D	IPR002081	Cryptochrome/DNA photolyase class 1	Family
A [auth C], B [auth A], C [auth B], D	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth B], D	IPR006050	DNA photolyase, N-terminal	Domain
A [auth C], B [auth A], C [auth B], D	IPR005101	Cryptochrome/DNA photolyase, FAD-binding 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.