1PK8 | pdb_00001pk8

Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP

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	d1pk8a1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1pk8a2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1pk8c1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1pk8c2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1pk8f1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1pk8f2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
H	d1pk8h1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
H	d1pk8h2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d1pk8g1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d1pk8g2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1pk8e1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1pk8e2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1pk8d1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1pk8d2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1pk8b1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin I	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1pk8b2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Synapsin domain	8026459	4003882	SCOP2 (2022-06-29)
A	SCOP2 Family	Synapsin C-terminal domain	8026462	4002060	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8038838	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8038841	3000094	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	RimK	e1pk8A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
A	Synapsin	e1pk8A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
C	RimK	e1pk8C1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
C	Synapsin	e1pk8C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
F	RimK	e1pk8F1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
F	Synapsin	e1pk8F2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
H	RimK	e1pk8H1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
H	Synapsin	e1pk8H2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
G	RimK	e1pk8G1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
G	Synapsin	e1pk8G2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
E	RimK	e1pk8E1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
E	Synapsin	e1pk8E2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
D	RimK	e1pk8D1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
D	Synapsin	e1pk8D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
B	RimK	e1pk8B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
B	Synapsin	e1pk8B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
F	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
F	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
H	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
H	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
H	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
G	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
G	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
E	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
E	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02750	Synapsin, ATP binding domain (Synapsin_C)	Synapsin, ATP binding domain	Ca dependent ATP binding in this ATP grasp fold. Function unknown.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	rat synapsin I	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding kinase binding enzyme binding protein kinase binding cytoskeletal protein binding actin binding calcium-dependent protein binding identical protein binding	trans-synaptic signaling regulation of biological process cellular localization neurotransmitter secretion transport signaling secretion biological regulation cell-cell signaling export from cell neurotransmitter transport establishment of localization cell communication chemical synaptic transmission localization trans-synaptic signaling regulation of biological process cellular localization neurotransmitter secretion transport signaling secretion biological regulation cell-cell signaling export from cell neurotransmitter transport establishment of localization cell communication chemical synaptic transmission localization signal release from synapse synaptic signaling secretion by cell signal release anterograde trans-synaptic signaling establishment of localization in cell cellular process cellular component organization cell junction organization synapse organization cellular component organization or biogenesis vesicle localization synaptic vesicle clustering synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse organelle localization synaptic vesicle localization regulation of localization regulated exocytosis regulation of cellular process modulation of chemical synaptic transmission synaptic vesicle exocytosis regulation of regulated secretory pathway regulation of secretion by cell regulation of signaling regulation of transport regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis regulation of vesicle-mediated transport regulation of secretion regulation of trans-synaptic signaling exocytosis regulation of neurotransmitter secretion regulation of exocytosis regulation of cell communication developmental process multicellular organismal process cellular developmental process cell development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development regulation of synaptic vesicle cycle	presynapse cellular anatomical structure synapse cell junction presynaptic active zone axon neuron projection axon terminus plasma membrane bounded cell projection cell projection distal axon terminal bouton neuron projection terminus somatodendritic compartment presynapse cellular anatomical structure synapse cell junction presynaptic active zone axon neuron projection axon terminus plasma membrane bounded cell projection cell projection distal axon terminal bouton neuron projection terminus somatodendritic compartment dendrite dendritic tree membrane-bounded organelle extrinsic component of synaptic vesicle membrane intracellular anatomical structure intracellular vesicle transport vesicle membrane extrinsic component of organelle membrane endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle membrane exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle secretory vesicle cytoplasm organelle membrane extrinsic component of membrane exocytic vesicle Golgi apparatus cytoskeleton membraneless organelle intracellular membraneless organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular organelle lumen organelle lumen synaptonemal structure synaptonemal complex condensed chromosome nuclear lumen postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse Schaffer collateral - CA1 synapse cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001359	Synapsin	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020897	Synapsin, pre-ATP-grasp domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019736	Synapsin, phosphorylation site	PTM
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019735	Synapsin, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020898	Synapsin, ATP-binding domain	Domain