4WB3 | pdb_00004wb3

Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Anaphylotoxins (complement system)	8070211	3000387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Anaphylotoxins (complement system)	8070211	3000387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Anaphylotoxins (complement system)	8070211	3000387	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	ANATO	e4wb3A1	A: few secondary structure elements	X: Anaphylotoxins (complement system) (From Topology)	H: Anaphylotoxins (complement system) (From Topology)	T: Anaphylotoxins (complement system)	F: ANATO	ECOD (1.6)
B	ANATO	e4wb3B1	A: few secondary structure elements	X: Anaphylotoxins (complement system) (From Topology)	H: Anaphylotoxins (complement system) (From Topology)	T: Anaphylotoxins (complement system)	F: ANATO	ECOD (1.6)
C	ANATO	e4wb3C1	A: few secondary structure elements	X: Anaphylotoxins (complement system) (From Topology)	H: Anaphylotoxins (complement system) (From Topology)	T: Anaphylotoxins (complement system)	F: ANATO	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.91.20	Mainly Alpha	Up-down Bundle	Influenza Virus Matrix Protein	Chain A, domain 1	CATH (4.3.0)
B	1.20.91.20	Mainly Alpha	Up-down Bundle	Influenza Virus Matrix Protein	Chain A, domain 1	CATH (4.3.0)
C	1.20.91.20	Mainly Alpha	Up-down Bundle	Influenza Virus Matrix Protein	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01821	Anaphylotoxin-like domain (ANATO)	Anaphylotoxin-like domain	C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins. ...	C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Complement C5	enzyme regulator activity peptidase activity peptidase regulator activity catalytic activity, acting on a protein hydrolase activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity molecular function inhibitor activity molecular function regulator activity catalytic activity endopeptidase activity	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process immune response biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus immune system process B cell mediated immunity regulation of immune response activation of immune response developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis positive regulation of multicellular organismal process biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response response to stress inflammatory response complement activation, alternative pathway response to biotic stimulus innate immune response response to external biotic stimulus response to other organism defense response to symbiont response to external stimulus defense response to other organism	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex pore complex membrane attack complex extracellular region extracellular space
D, E	mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR009048	Alpha-macroglobulin, receptor-binding	Domain
A, B, C	IPR041555	Macroglobulin domain MG3	Domain
A, B, C	IPR001599	Alpha-2-macroglobulin	Domain
A, B, C	IPR048843	Complement component 5, CUB domain	Domain
A, B, C	IPR018081	Anaphylatoxin, complement system	Homologous Superfamily
A, B, C	IPR018933	Netrin module, non-TIMP type	Domain
A, B, C	IPR041425	Complement C3/4/5, macroglobulin domain MG1	Domain
A, B, C	IPR011625	Alpha-2-macroglobulin, bait region domain	Domain
A, B, C	IPR001134	Netrin domain	Domain
A, B, C	IPR008993	Tissue inhibitor of metalloproteinases-like, OB-fold	Homologous Superfamily
A, B, C	IPR011626	Alpha-macroglobulin-like, TED domain	Domain
A, B, C	IPR000020	Anaphylatoxin/fibulin	Domain
A, B, C	IPR036595	Alpha-macroglobulin, receptor-binding domain superfamily	Homologous Superfamily
A, B, C	IPR002890	Macroglobulin domain	Domain
A, B, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C	IPR050473	Alpha-2-macroglobulin/Complement system	Family
A, B, C	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily
A, B, C	IPR040839	Macroglobulin domain MG4	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.