9NFU | pdb_00009nfu

CryoEM Structure of De Novo Antibody Fragment scFv 6 with C. difficile Toxin B (TcdB)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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	Nucleotide-diphospho-sugar transferases	8033597	3000077	SCOP2B (2022-06-29)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	scFv 6 Heavy Chain, scFv 6 Light Chain	-	-	-
A	Toxin B	binding lipid binding toxin activity glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding binding lipid binding toxin activity glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host actin cytoskeleton symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization symbiont-mediated perturbation of host cytoskeleton disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region host cell plasma membrane host cell cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
A	IPR024772	TcdA/TcdB toxin, N-terminal helical domain	Domain
A	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
A	IPR024769	TcdA/TcdB toxin, pore forming domain	Domain
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A	IPR024770	TcdA/TcdB toxin, catalytic glycosyltransferase domain	Domain
A	IPR018337	Cell wall/choline-binding repeat	Repeat

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.