6XFQ | pdb_00006xfq

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)
C [auth B]	SCOP2B Superfamily	C-type lectin-like	8065478	3001261	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	C-type lectin-like	8065518	3001261	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	L domain-like	8034703	3001010	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)
C [auth B]	Lectin_C	e6xfqB1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: Lectin_C	ECOD (1.6)
B [auth A]	Lectin_C	e6xfqA1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: Lectin_C	ECOD (1.6)
A [auth G]	LRR_8_1	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: LRR_8_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B]	Snaclec agglucetin subunit beta-2	toxin activity	-	cellular anatomical structure extracellular region
B [auth A]	Snaclec agglucetin subunit alpha-1	toxin activity	-	cellular anatomical structure extracellular region
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 signaling receptor activity transmembrane 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 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 establishment of localization maintenance of location transmembrane transport release of sequestered calcium ion into cytosol cellular homeostasis chemical homeostasis calcium ion transmembrane transport cell adhesion protein maturation blood coagulation, intrinsic pathway blood coagulation, fibrin clot formation protein metabolic process protein activation cascade primary metabolic process gene expression macromolecule biosynthetic process biosynthetic process metabolic process macromolecule metabolic process positive regulation of biological process regulation of cell activation positive regulation of platelet activation positive regulation of cell activation positive regulation of cellular process regulation of platelet activation positive regulation of multicellular organismal process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	IPR050111	C-type lectin and snaclec domain-containing protein	Family
C [auth B]	IPR016187	C-type lectin fold	Homologous Superfamily
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]	IPR050111	C-type lectin and snaclec domain-containing protein	Family
B [auth A]	IPR016187	C-type lectin fold	Homologous Superfamily
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

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 R01GM157729.