1MQS | pdb_00001mqs

Crystal structure of Sly1p in complex with an N-terminal peptide of Sed5p

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1mqsa_	Multi-domain proteins (alpha and beta)	Sec1/munc18-like (SM) proteins	Sec1/munc18-like (SM) proteins	Sec1/munc18-like (SM) proteins	Sly1P protein	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Sec1/munc18-like (SM) proteins	8031377	4002933	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sec1/munc18-like	8043755	3001920	SCOP2 (2022-06-29)
B	SCOP2 Family	Syntaxin-5 N-terminal domain-like	8046401	4005062	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Syntaxin-5 N-terminal region-like	8054411	3002290	SCOP2 (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	Sec1_3rd	e1mqsA1	A: alpha complex topology	X: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	H: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	T: alpha-helical domain in sec1/munc18-like (SM) proteins	F: Sec1_3rd	ECOD (1.6)
A	Sec1_1st_1	e1mqsA2	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_1st_1	ECOD (1.6)
A	Sec1_2nd	e1mqsA3	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 1	CATH (4.3.0)
A	3.40.50.1910	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 2	CATH (4.3.0)
A	3.90.830.10	Alpha Beta	Alpha-Beta Complex	Syntaxin Binding Protein 1	Chain A, domain 2	CATH (4.3.0)
A	1.25.40.60	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00995	Sec1 family (Sec1)	Sec1 family	-	Family
B	PF11416	Syntaxin-5 N-terminal, Sly1p-binding domain (Syntaxin-5_N)	Syntaxin-5 N-terminal, Sly1p-binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sly1 Protein	protein binding binding SNARE binding syntaxin binding	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Golgi vesicle transport vesicle-mediated transport positive regulation of organelle organization regulation of localization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization membrane fusion organelle membrane fusion positive regulation of biological process regulation of vesicle fusion cellular component organization cellular component biogenesis vesicle organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly positive regulation of SNARE complex assembly SNARE complex assembly cellular component organization or biogenesis positive regulation of cellular process membrane organization regulation of biological process protein-containing complex organization regulation of transport positive regulation of cellular component biogenesis biological regulation regulation of cellular component biogenesis regulation of vesicle-mediated transport regulation of organelle organization organelle fusion organelle organization regulation of SNARE complex assembly positive regulation of transport positive regulation of vesicle fusion vesicle fusion cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction Ras protein signal transduction regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of Ras protein signal transduction intracellular signaling cassette regulation of cell communication signal transduction endoplasmic reticulum to Golgi vesicle-mediated transport vesicle fusion with Golgi apparatus Golgi organization endomembrane system organization	cellular anatomical structure membrane membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane cytosol cellular anatomical structure membrane membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane cytosol intracellular vesicle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle coated vesicle vesicle endoplasmic reticulum
B	Integral Membrane Protein SED5	protein binding binding SNARE binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport regulation of biological process regulation of cellular process regulation of cellular component organization regulation of inclusion body assembly biological regulation inclusion body assembly regulation of cellular component biogenesis localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport regulation of biological process regulation of cellular process regulation of cellular component organization regulation of inclusion body assembly biological regulation inclusion body assembly regulation of cellular component biogenesis cellular component biogenesis cellular component organization cellular component assembly cellular component organization or biogenesis protein localization cellular localization establishment of protein localization nitrogen compound transport intracellular transport protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization intracellular protein transport membrane organization membrane fusion organelle membrane fusion vesicle organization organelle fusion organelle organization vesicle fusion endoplasmic reticulum to Golgi vesicle-mediated transport vesicle fusion with Golgi apparatus Golgi organization endomembrane system organization organelle localization by membrane tethering organelle localization vesicle docking membrane docking	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm membrane Golgi membrane bounding membrane of organelle organelle membrane cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm membrane Golgi membrane bounding membrane of organelle organelle membrane Golgi cis cisterna membrane Golgi cisterna membrane Golgi apparatus subcompartment organelle subcompartment Golgi cisterna Golgi cis cisterna Golgi stack SNARE complex protein-containing complex membrane protein complex endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR043154	Sec1-like, domain 1	Homologous Superfamily
A	IPR036045	Sec1-like superfamily	Homologous Superfamily
A	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
A	IPR001619	Sec1-like protein	Family
B	IPR021538	Syntaxin-5, N-terminal, Sly1p-binding domain	Domain
B	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
B	IPR000727	Target SNARE coiled-coil homology domain	Domain
B	IPR010989	SNARE	Homologous Superfamily
B	IPR045242	Syntaxin	Family

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.