3FDW | pdb_00003fdw

Crystal structure of a C2 domain from human synaptotagmin-like protein 4

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3fdwa_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3fdwb_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Synaptotagmin-like (S variant)	8072596	4002234	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8072597	3000965	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8072597	3000965	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	Thioesterase	e3fdwA1	A: alpha bundles	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Thioesterase	ECOD (develop294)
B	IL7	e3fdwB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Synaptotagmin-like protein 4	small GTPase binding protein binding binding enzyme binding GTPase binding phospholipid binding lipid binding signaling receptor binding neurexin family protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small GTPase binding protein binding binding enzyme binding GTPase binding phospholipid binding lipid binding signaling receptor binding neurexin family protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	localization organelle localization lysosome localization vacuolar localization regulation of localization regulation of cellular process transport positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis vesicle-mediated transport regulation of secretion by cell secretion by cell positive regulation of secretion localization organelle localization lysosome localization vacuolar localization regulation of localization regulation of cellular process transport positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis vesicle-mediated transport regulation of secretion by cell secretion by cell positive regulation of secretion positive regulation of cellular process regulation of biological process regulation of transport secretion biological regulation export from cell regulation of vesicle-mediated transport establishment of localization regulation of secretion positive regulation of transport exocytosis regulation of exocytosis cellular process negative regulation of protein transport establishment of protein localization nitrogen compound transport negative regulation of biological process negative regulation of transport cell communication negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell intracellular protein localization regulation of biological quality regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion regulation of protein secretion negative regulation of protein secretion regulation of hormone secretion regulation of protein localization regulation of peptide secretion signaling negative regulation of signaling hormone secretion negative regulation of cell communication protein localization to extracellular region negative regulation of peptide secretion peptide secretion signal release negative regulation of cellular process negative regulation of protein localization regulation of signaling regulation of peptide transport regulation of establishment of protein localization cell-cell signaling regulation of protein transport peptide transport negative regulation of insulin secretion protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion membrane organization wound healing regulation of cellular component organization response to stimulus plasma membrane repair cellular component organization regulation of plasma membrane organization response to stress plasma membrane organization regulation of plasma membrane repair cellular component organization or biogenesis response to wounding endomembrane system organization cellular localization intracellular transport establishment of localization in cell intracellular protein transport multivesicular body sorting pathway positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of protein secretion positive regulation of protein localization	membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle cell periphery plasma membrane membrane platelet alpha granule membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane secretory granule organelle membrane platelet alpha granule secretory granule membrane endosome transport vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000008	C2 domain	Domain
A, B	IPR010911	Rab-binding domain	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR001565	Synaptotagmin	Domain
A, B	IPR037303	Synaptotagmin-like protein 4/5, C2A domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR044134	Synaptotagmin-like protein 4 , FYVE-related domain	Domain
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B	IPR043567	Synaptotagmin-like 1-5, C2B domain	Domain
A, B	IPR041282	FYVE-type zinc finger	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q96C24	astrocytic tumor glioblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma atypical teratoid rhabdoid tumor intellectual disability malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida exocrine pancreatic carcinoma astrocytic tumor glioblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma atypical teratoid rhabdoid tumor intellectual disability malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida exocrine pancreatic carcinoma large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	All beta monotopic/peripheral	C2 domain	C2 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.