1K9A | pdb_00001k9a

Crystal structure analysis of full-length carboxyl-terminal Src kinase at 2.5 A resolution

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	d1k9aa1	All beta proteins	SH3-like barrel	SH3-domain	SH3-domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1k9aa2	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1k9aa3	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1k9ab1	All beta proteins	SH3-like barrel	SH3-domain	SH3-domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1k9ab2	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1k9ab3	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1k9ac1	All beta proteins	SH3-like barrel	SH3-domain	SH3-domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1k9ac2	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1k9ac3	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1k9ad1	All beta proteins	SH3-like barrel	SH3-domain	SH3-domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1k9ad2	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1k9ad3	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1k9ae1	All beta proteins	SH3-like barrel	SH3-domain	SH3-domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1k9ae2	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1k9ae3	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1k9af1	All beta proteins	SH3-like barrel	SH3-domain	SH3-domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1k9af2	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Carboxyl-terminal src kinase (csk)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1k9af3	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Carboxyl-terminal src kinase (csk)	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	SH3-domain	8027729	4000369	SCOP2 (2022-06-29)
A	SCOP2 Family	SH2 domain	8027730	4001650	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SH3-domain	8040108	3000153	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SH2 domain	8040109	3000197	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SH2 domain	8040109	3000197	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8040108	3000153	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH3-domain	8040108	3000153	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH2 domain	8040109	3000197	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SH3-domain	8040108	3000153	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SH2 domain	8040109	3000197	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SH3-domain	8040108	3000153	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SH2 domain	8040109	3000197	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	SH3-domain	8040108	3000153	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	SH2 domain	8040109	3000197	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	SH3_1	e1k9aA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
A	SH2	e1k9aA2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
A	Pkinase_Tyr	e1k9aA3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
B	SH3_1	e1k9aB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
B	SH2	e1k9aB2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
B	Pkinase_Tyr	e1k9aB3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
C	SH3_1	e1k9aC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
C	SH2	e1k9aC2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
C	Pkinase_Tyr	e1k9aC3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
D	SH3_1	e1k9aD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
D	SH2	e1k9aD2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
D	Pkinase_Tyr	e1k9aD3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
E	SH3_1	e1k9aE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
E	SH2	e1k9aE2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
E	Pkinase_Tyr	e1k9aE3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
F	SH3_1	e1k9aF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
F	SH2	e1k9aF2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
F	Pkinase_Tyr	e1k9aF3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
A	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
C	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
D	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
E	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
E	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
E	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
E	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
F	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
F	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
F	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
F	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	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	PF00017	SH2 domain (SH2)	SH2 domain		Domain
A, B, C, D, E A, B, C, D, E, F	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain
A, B, C, D, E A, B, C, D, E, F	PF07714	Protein tyrosine and serine/threonine kinase (PK_Tyr_Ser-Thr)	Protein tyrosine and serine/threonine kinase	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphospha ...	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [1]; Serine/threonine-protein kinases, tyrosine-protein kinases, and dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins). This entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include the catalytic domain of dual specificity kinases.	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	Carboxyl-terminal Src kinase	catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity histone H3Y41 kinase activity histone H3 kinase activity histone modifying activity catalytic activity histone kinase activity protein phosphatase binding phosphatase binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity histone H3Y41 kinase activity histone H3 kinase activity histone modifying activity catalytic activity histone kinase activity protein phosphatase binding phosphatase binding protein binding binding enzyme 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 proline-rich region binding non-membrane spanning protein tyrosine kinase activity protein kinase A catalytic subunit binding protein kinase A binding kinase binding protein kinase binding histone H2AXY142 kinase activity histone H2AX kinase activity protein tyrosine kinase binding cation binding metal ion binding identical protein binding	adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization negative regulation of protein transport protein localization regulation of localization Golgi to plasma membrane transport establishment of protein localization nitrogen compound transport regulation of cellular process negative regulation of biological process adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization negative regulation of protein transport protein localization regulation of localization Golgi to plasma membrane transport establishment of protein localization nitrogen compound transport regulation of cellular process negative regulation of biological process establishment of protein localization to plasma membrane negative regulation of transport Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization regulation of biological process protein localization to cell periphery establishment of protein localization to membrane negative regulation of establishment of protein localization regulation of protein localization to cell periphery localization within membrane protein localization to membrane establishment of localization negative regulation of protein localization to membrane regulation of Golgi to plasma membrane protein transport negative regulation of Golgi to plasma membrane protein transport Golgi vesicle transport cellular localization post-Golgi vesicle-mediated transport regulation of protein localization transport negative regulation of protein localization to plasma membrane negative regulation of cellular process regulation of protein localization to membrane negative regulation of protein localization regulation of transport protein localization to plasma membrane biological regulation regulation of establishment of protein localization regulation of protein transport regulation of vesicle-mediated transport vesicle-mediated transport to the plasma membrane protein transport regulation of cellular localization macromolecule localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane developmental process multicellular organismal process cellular developmental process nervous system development multicellular organism development neurogenesis central nervous system development gliogenesis oligodendrocyte differentiation glial cell differentiation cell differentiation anatomical structure development system development response to stimulus immune response immune system process adaptive immune response interleukin-6 production regulation of interleukin-6 production regulation of cytokine production cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to hormone stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade regulation of plasma lipoprotein particle levels regulation of low-density lipoprotein particle clearance negative regulation of low-density lipoprotein particle clearance plasma lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance low-density lipoprotein particle clearance negative regulation of tissue remodeling homeostatic process negative regulation of bone remodeling regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption negative regulation of bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation import into cell regulation of cellular component organization negative regulation of endocytosis negative regulation of phagocytosis phagocytosis regulation of endocytosis negative regulation of cellular component organization regulation of phagocytosis endocytosis immune response-regulating cell surface receptor signaling pathway positive regulation of biological process positive regulation of response to stimulus regulation of Fc receptor mediated stimulatory signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of immune response activation of immune response	cell-cell junction cellular anatomical structure anchoring junction cell junction cell periphery plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D, E A, B, C, D, E, F	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR035027	CSK-like, SH2 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000980	SH2 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000719	Protein kinase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001452	SH3 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050198	Non-receptor tyrosine kinases involved in cell signaling	Family