1CSK - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP

Authors :   M. Mathieu, R. K. Wierenga

Date :   22 Mar 94 (Deposition) - 31 Jul 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. V. Borchert, M. Mathieu, J. P. Zeelen, S. A. Courtneidge, R. K. Wierenga
The Crystal Structure Of Human Csksh3: Structural Diversity Near The Rt-Src And N-Src Loop.
Febs Lett. V. 341 79 1994
PubMed-ID: 7511113 | Reference-DOI: 10.1016/0014-5793(94)80244-0
(for further references see the PDB file header)

Molecule 1 - C-SRC SH3 DOMAIN
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.112
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1CSK)

(no "Site" information available for 1CSK)

(no "SS Bond" information available for 1CSK)

(no "Cis Peptide Bond" information available for 1CSK)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041678	P	45	L	CSK_HUMAN	Polymorphism	---	A/B/C/D	P	45	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041678	P	45	L	CSK_HUMAN	Polymorphism	---	A	P	45	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041678	P	45	L	CSK_HUMAN	Polymorphism	---	B	P	45	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041678	P	45	L	CSK_HUMAN	Polymorphism	---	C	P	45	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041678	P	45	L	CSK_HUMAN	Polymorphism	---	D	P	45	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1CSK)

Asymmetric Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000220003	1b	ENSE00001357268	chr15:75074425-75075061	637	CSK_HUMAN	-	0	0	-	-
1.2	ENST00000220003	2	ENSE00001357265	chr15:75090574-75090653	80	CSK_HUMAN	1-5	5	0	-	-
1.3	ENST00000220003	3	ENSE00001326572	chr15:75090956-75091069	114	CSK_HUMAN	6-43	38	4	A:11-43 B:11-43 C:11-43 D:11-43	33 33 33 33
1.4	ENST00000220003	4	ENSE00001245986	chr15:75091167-75091279	113	CSK_HUMAN	44-81	38	4	A:44-68 B:44-68 C:44-68 D:44-68	25 25 25 25
1.5b	ENST00000220003	5b	ENSE00001245980	chr15:75091613-75091832	220	CSK_HUMAN	81-154	74	0	-	-
1.6	ENST00000220003	6	ENSE00001245972	chr15:75092753-75092846	94	CSK_HUMAN	155-186	32	0	-	-
1.7	ENST00000220003	7	ENSE00001245968	chr15:75093022-75093087	66	CSK_HUMAN	186-208	23	0	-	-
1.8	ENST00000220003	8	ENSE00001245963	chr15:75093164-75093263	100	CSK_HUMAN	208-241	34	0	-	-
1.9	ENST00000220003	9	ENSE00001245953	chr15:75093353-75093443	91	CSK_HUMAN	241-271	31	0	-	-
1.10	ENST00000220003	10	ENSE00001245942	chr15:75093863-75093936	74	CSK_HUMAN	272-296	25	0	-	-
1.11	ENST00000220003	11	ENSE00001163016	chr15:75094036-75094231	196	CSK_HUMAN	296-361	66	0	-	-
1.12	ENST00000220003	12	ENSE00001245924	chr15:75094338-75094424	87	CSK_HUMAN	362-390	29	0	-	-
1.13b	ENST00000220003	13b	ENSE00001870511	chr15:75094672-75095539	868	CSK_HUMAN	391-450	60	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:58
 aligned with CSK_HUMAN | P41240 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:58
                                    20        30        40        50        60        
             CSK_HUMAN   11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
               SCOP domains d1cska_ A: Carboxyl-terminal src kinase (csk)              SCOP domains
               CATH domains 1cskA00 A:11-68 SH3 Domains                                CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee.....eeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------L----------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:11-43           Exon 1.4  PDB: A:44-68    Transcript 1
                  1csk A 11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
                                    20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with CSK_HUMAN | P41240 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:58
                                    20        30        40        50        60        
             CSK_HUMAN   11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
               SCOP domains d1cskb_ B: Carboxyl-terminal src kinase (csk)              SCOP domains
               CATH domains 1cskB00 B:11-68 SH3 Domains                                CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee.....eeeeee....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------L----------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: B:11-43           Exon 1.4  PDB: B:44-68    Transcript 1
                  1csk B 11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
                                    20        30        40        50        60

Chain C from PDB  Type:PROTEIN  Length:58
 aligned with CSK_HUMAN | P41240 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:58
                                    20        30        40        50        60        
             CSK_HUMAN   11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
               SCOP domains d1cskc_ C: Carboxyl-terminal src kinase (csk)              SCOP domains
               CATH domains 1cskC00 C:11-68 SH3 Domains                                CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee.....eeeeee....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------L----------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: C:11-43           Exon 1.4  PDB: C:44-68    Transcript 1
                  1csk C 11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
                                    20        30        40        50        60

Chain D from PDB  Type:PROTEIN  Length:58
 aligned with CSK_HUMAN | P41240 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:58
                                    20        30        40        50        60        
             CSK_HUMAN   11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
               SCOP domains d1cskd_ D: Carboxyl-terminal src kinase (csk)              SCOP domains
               CATH domains 1cskD00 D:11-68 SH3 Domains                                CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee.....eeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------L----------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: D:11-43           Exon 1.4  PDB: D:44-68    Transcript 1
                  1csk D 11 GTECIAKYNFHGTAEQDLPFCKGDVLTIVAVTKDPNWYKAKNKVGREGIIPANYVQKR 68
                                    20        30        40        50        60

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: SH3-domain (369)

Family: SH3-domain (255)

Protein domain: Carboxyl-terminal src kinase (csk) (3)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1cska_	A:
1b	d1cskb_	B:
1c	d1cskc_	C:
1d	d1cskd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Human (Homo sapiens) (133)

1a	1cskA00	A:11-68
1b	1cskB00	B:11-68
1c	1cskC00	C:11-68
1d	1cskD00	D:11-68

(no "Pfam Domain" information available for 1CSK)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CSK_HUMAN | P41240)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004715	non-membrane spanning protein tyrosine kinase activity	Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0070064	proline-rich region binding	Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0034236	protein kinase A catalytic subunit binding	Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0034332	adherens junction organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0071375	cellular response to peptide hormone stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
	GO:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0007173	epidermal growth factor receptor signaling pathway	A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0070373	negative regulation of ERK1 and ERK2 cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0042997	negative regulation of Golgi to plasma membrane protein transport	Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
	GO:0045779	negative regulation of bone resorption	Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0032715	negative regulation of interleukin-6 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
	GO:0033673	negative regulation of kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0010989	negative regulation of low-density lipoprotein particle clearance	Any process that decreases the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
	GO:0050765	negative regulation of phagocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis.
	GO:0048709	oligodendrocyte differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
	GO:0038083	peptidyl-tyrosine autophosphorylation	The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0060368	regulation of Fc receptor mediated stimulatory signaling pathway	Any process that modulates the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway. The Fc receptor mediated stimulatory signaling pathway is a series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0001817	regulation of cytokine production	Any process that modulates the frequency, rate, or extent of production of a cytokine.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	1csk
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	CSK_HUMAN \| P41240	:	1byg 3d7t 3d7u 3eac 3eaz

(no "Related Entries Specified in the PDB File" available for 1CSK)

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