6XFQ

Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth G]	SCOP2B Superfamily	L domain-like	8034703	3001010	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	C-type lectin-like	8065518	3001261	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	C-type lectin-like	8065478	3001261	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 [auth G]	PF01462,PF13855	e6xfqG1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: PF01462,PF13855	ECOD (1.6)
B [auth A]	PF00059	e6xfqA1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
C [auth B]	PF00059	e6xfqB1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G]	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A [auth G]	PF01462	Leucine rich repeat N-terminal domain (LRRNT)	Leucine rich repeat N-terminal domain	-	Family
B [auth A]	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain
C [auth B]	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G]	Platelet glycoprotein Ib alpha chain	peptide receptor activity molecular transducer activity G protein-coupled receptor activity thrombin-activated receptor activity proteinase-activated receptor activity G protein-coupled peptide receptor activity transmembrane signaling receptor activity signaling receptor activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding developmental process cellular developmental process hemopoiesis multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding developmental process cellular developmental process hemopoiesis megakaryocyte differentiation cell development myeloid cell differentiation cell differentiation megakaryocyte development anatomical structure development myeloid cell development cellular process regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis regulation of biological process negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process cell activation platelet activation cellular response to stimulus regulation of cellular process cell surface receptor signaling pathway signaling signal transduction cell communication anatomical structure morphogenesis cell morphogenesis regulation of cell motility positive regulation of biological process positive regulation of leukocyte cell-cell adhesion regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion leukocyte tethering or rolling positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion positive regulation of leukocyte tethering or rolling cellular extravasation regulation of cell migration regulation of cell-cell adhesion cell migration regulation of immune system process cell motility locomotion positive regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion regulation of leukocyte migration positive regulation of leukocyte adhesion to vascular endothelial cell leukocyte migration regulation of leukocyte tethering or rolling leukocyte adhesion to vascular endothelial cell immune system process regulation of locomotion regulation of leukocyte cell-cell adhesion regulation of cellular extravasation regulation of localization cellular localization inorganic ion homeostasis intracellular calcium ion homeostasis transport homeostatic process monoatomic ion transmembrane transport calcium ion homeostasis negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell monoatomic cation transmembrane transport localization intracellular monoatomic cation homeostasis monoatomic ion homeostasis negative regulation of cellular process monoatomic ion transport intracellular chemical homeostasis monoatomic cation homeostasis monoatomic cation transport regulation of sequestering of calcium ion intracellular monoatomic ion homeostasis calcium ion transmembrane import into cytosol sequestering of calcium ion inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol cellular homeostasis chemical homeostasis calcium ion transmembrane transport cellular biosynthetic process protein maturation organic substance metabolic process blood coagulation, intrinsic pathway blood coagulation, fibrin clot formation organic substance biosynthetic process protein metabolic process protein activation cascade organonitrogen compound metabolic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process biosynthetic process metabolic process macromolecule metabolic process regulation of cell activation positive regulation of platelet activation positive regulation of cell activation regulation of platelet activation positive regulation of multicellular organismal process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure protein-containing complex plasma membrane protein complex membrane protein complex glycoprotein Ib-IX-V complex receptor complex glycoprotein complex plasma membrane signaling receptor complex
B [auth A]	Snaclec agglucetin subunit alpha-1	toxin activity	-	extracellular region cellular anatomical entity
C [auth B]	Snaclec agglucetin subunit beta-2	toxin activity	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G]	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A [auth G]	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A [auth G]	IPR001611	Leucine-rich repeat	Repeat
A [auth G]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A [auth G]	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
B [auth A]	IPR001304	C-type lectin-like	Domain
B [auth A]	IPR018378	C-type lectin, conserved site	Conserved Site
B [auth A]	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
B [auth A]	IPR016187	C-type lectin fold	Homologous Superfamily
C [auth B]	IPR001304	C-type lectin-like	Domain
C [auth B]	IPR018378	C-type lectin, conserved site	Conserved Site
C [auth B]	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
C [auth B]	IPR016187	C-type lectin fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth G]	Pharos: P07359	Bernard-Soulier syndrome Bernard-Soulier syndrome, type A2, autosomal dominant pseudo-von Willebrand disease nonarteritic anterior ischemic optic neuropathy, susceptibility to thrombotic disease hypertensive disorder Von Willebrand disease, platelet type attention deficit hyperactivity disorder, inattentive type brain aneurysm hereditary von Willebrand disease non-arteritic anterior ischemic optic neuropathy thrombocytopenia osteosarcoma

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 R01GM133198.