2FPD | pdb_00002fpd

Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	SH3-domain	8072709	3000153	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH3-domain	8072709	3000153	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8072709	3000153	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SH3-domain	8072709	3000153	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)
D		e2fpdD1	A: ADP-ribosylation	X: ADP-ribosylation	H: ADP-ribosylation	T: SH3_9	F:	ECOD (20:10:01)
C		e2fpdC1	A: Restriction endonuclease-like	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: RE_AlwI	F:	ECOD (20:10:01)
B		e2fpdB1	A: Carbon-nitrogen hydrolase-like	X: Rubredoxin-related	H: Rubredoxin-related	T:	F:	ECOD (20:10:01)
A		e2fpdA1	A: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	X: Snake toxin-like	H: Snake toxin-like	T: UPAR_LY6	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
C	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF14604	Variant SH3 domain (SH3_9)	Variant SH3 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	C-jun-amino-terminal kinase interacting protein 1	JUN kinase binding protein binding binding kinase binding enzyme binding protein kinase binding cytoskeletal protein binding kinesin binding mitogen-activated protein kinase kinase binding MAP-kinase scaffold activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity mitogen-activated protein kinase kinase kinase binding JUN kinase binding protein binding binding kinase binding enzyme binding protein kinase binding cytoskeletal protein binding kinesin binding mitogen-activated protein kinase kinase binding MAP-kinase scaffold activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity mitogen-activated protein kinase kinase kinase binding identical protein binding	cellular response to stimulus regulation of cellular process response to stimulus regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of signal transduction regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction regulation of primary metabolic process cell communication negative regulation of kinase activity negative regulation of JNK cascade JNK cascade cellular response to stimulus regulation of cellular process response to stimulus regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of signal transduction regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction regulation of primary metabolic process cell communication negative regulation of kinase activity negative regulation of JNK cascade JNK cascade phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process signal transduction phosphorus metabolic process protein modification process negative regulation of protein metabolic process regulation of biological process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process regulation of JNK cascade primary metabolic process regulation of MAPK cascade regulation of molecular function regulation of kinase activity regulation of response to stimulus negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process negative regulation of cell communication regulation of intracellular signal transduction negative regulation of protein serine/threonine kinase activity negative regulation of cellular process protein metabolic process negative regulation of JUN kinase activity negative regulation of macromolecule metabolic process regulation of signaling negative regulation of response to stimulus biological regulation negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process negative regulation of protein kinase activity negative regulation of signal transduction negative regulation of phosphorus metabolic process regulation of JUN kinase activity MAPK cascade regulation of cell communication regulation of phosphorylation cellular process negative regulation of phosphorylation negative regulation of MAPK cascade negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process positive regulation of response to stimulus positive regulation of JNK cascade positive regulation of cellular process positive regulation of MAPK cascade positive regulation of intracellular signal transduction positive regulation of signaling RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription localization transport establishment of localization vesicle-mediated transport multicellular organismal process CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation regulation of leukocyte activation CD8-positive, alpha-beta T cell proliferation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation regulation of alpha-beta T cell proliferation T cell activation alpha-beta T cell proliferation lymphocyte proliferation alpha-beta T cell activation regulation of immune system process regulation of multicellular organismal process T cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation regulation of CD8-positive, alpha-beta T cell proliferation cell population proliferation cell activation regulation of T cell activation regulation of T cell proliferation immune system process mononuclear cell proliferation regulation of cell population proliferation regulation of mononuclear cell proliferation regulation of CD8-positive, alpha-beta T cell activation regulation of lymphocyte activation	growth cone axon cell projection cellular anatomical structure distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth membrane membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion growth cone axon cell projection cellular anatomical structure distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth membrane membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion intracellular membrane-bounded organelle intracellular organelle organelle envelope organelle mitochondrial envelope cytoplasm organelle membrane cytosol dendrite terminus somatodendritic compartment dendritic growth cone dendrite dendritic tree cell periphery plasma membrane organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane synapse cell junction perinuclear region of cytoplasm cell body neuronal cell body dentate gyrus mossy fiber hippocampal mossy fiber nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035638	JIP1, SH3 domain	Domain
A, B, C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR047178	JNK-interacting protein 1	Family
A, B, C, D	IPR006020	PTB/PI domain	Domain
A, B, C, D	IPR001452	SH3 domain	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.