5DJU

Crystal structure of LOV2 (C450A) domain in complex with Zdk3

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)
A [auth B]	d5djub_	All alpha proteins	immunoglobulin/albumin-binding domain-like	Bacterial immunoglobulin/albumin-binding domains	Immunoglobulin-binding protein A modules	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C [auth D]	d5djud_	All alpha proteins	immunoglobulin/albumin-binding domain-like	Bacterial immunoglobulin/albumin-binding domains	Immunoglobulin-binding protein A modules	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	B	e5djuB1	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Bacterial immunoglobulin/albumin-binding domains (From Topology)	T: Bacterial immunoglobulin/albumin-binding domains	F: B	ECOD (1.6)
C [auth D]	B	e5djuD1	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Bacterial immunoglobulin/albumin-binding domains (From Topology)	T: Bacterial immunoglobulin/albumin-binding domains	F: B	ECOD (1.6)
D [auth C]	PAS	e5djuC1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS	ECOD (1.6)
B [auth A]	PAS	e5djuA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (4.3.0)
C [auth D]	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (4.3.0)
D [auth C]	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
B [auth A]	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], D [auth C]	PF13426	PAS domain (PAS_9)	PAS domain	This domain is found in many signalling proteins in which it functions as a sensor domain. It recognises FMN, Zn(II), FAD and riboflavin (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 [auth B], C [auth D]	Engineered protein, Zdk3 affibody	-	-	-
B [auth A], D [auth C]	NPH1-2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups blue light photoreceptor activity molecular transducer activity photoreceptor activity signaling receptor activity cation binding metal ion binding	-	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], D [auth C]	IPR017441	Protein kinase, ATP binding site	Binding Site
B [auth A], D [auth C]	IPR000014	PAS domain	Domain
B [auth A], D [auth C]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth A], D [auth C]	IPR035965	PAS domain superfamily	Homologous Superfamily
B [auth A], D [auth C]	IPR001610	PAC motif	Repeat
B [auth A], D [auth C]	IPR000700	PAS-associated, C-terminal	Domain
B [auth A], D [auth C]	IPR000719	Protein kinase domain	Domain
B [auth A], D [auth C]	IPR008271	Serine/threonine-protein kinase, active site	Active Site

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.