1B07 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR

Authors :   J. T. Nguyen, C. W. Turck, F. E. Cohen, R. N. Zuckermann, W. A. Lim

Date :   17 Nov 98 (Deposition) - 06 Jan 99 (Release) - 25 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,C

Keywords :   Sh3 Domain, Inhibitors, Peptoids, Protein-Protein Recognition, Proline-Rich Motifs, Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. T. Nguyen, C. W. Turck, F. E. Cohen, R. N. Zuckermann, W. A. Lim
Exploiting The Basis Of Proline Recognition By Sh3 And Ww Domains: Design Of N-Substituted Inhibitors.
Science V. 282 2088 1998
PubMed-ID: 9851931 | Reference-DOI: 10.1126/SCIENCE.282.5396.2088

Molecule 1 - PROTEIN (PROTO-ONCOGENE CRK (CRK))
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	TG1
	Expression System Taxid	:	562
	Fragment	:	SH3 DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	P38, ADAPTER MOLECULE CRK

Molecule 2 - PROTEIN (SH3 PEPTOID INHIBITOR)
	Chains	:	C
	Engineered	:	YES

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PYJ	1	Ligand/Ion	PHENYLETHANE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:158 , ARG A:160 , GLU A:173 , ASP A:174 , SER A:175 , PRO C:4 , GLY C:5	BINDING SITE FOR RESIDUE PYJ C 1005

(no "SS Bond" information available for 1B07)

(no "Cis Peptide Bond" information available for 1B07)

(no "SAP(SNP)/Variant" information available for 1B07)

(no "PROSITE Motif" information available for 1B07)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSMUST00000068714	1	ENSMUSE00000358919	chr17:80879793-80879177	617	SOS1_MOUSE	1-29	29	0	-	-
1.2	ENSMUST00000068714	2	ENSMUSE00000401901	chr17:80859387-80859262	126	SOS1_MOUSE	30-71	42	0	-	-
1.3	ENSMUST00000068714	3	ENSMUSE00000140174	chr17:80854523-80854392	132	SOS1_MOUSE	72-115	44	0	-	-
1.4	ENSMUST00000068714	4	ENSMUSE00000539699	chr17:80853260-80853096	165	SOS1_MOUSE	116-170	55	0	-	-
1.5	ENSMUST00000068714	5	ENSMUSE00000140173	chr17:80851530-80851321	210	SOS1_MOUSE	171-240	70	0	-	-
1.6	ENSMUST00000068714	6	ENSMUSE00000140175	chr17:80848741-80848598	144	SOS1_MOUSE	241-288	48	0	-	-
1.7	ENSMUST00000068714	7	ENSMUSE00000140170	chr17:80845052-80844942	111	SOS1_MOUSE	289-325	37	0	-	-
1.8	ENSMUST00000068714	8	ENSMUSE00000539693	chr17:80844868-80844770	99	SOS1_MOUSE	326-358	33	0	-	-
1.9	ENSMUST00000068714	9	ENSMUSE00000140161	chr17:80834362-80834235	128	SOS1_MOUSE	359-401	43	0	-	-
1.10	ENSMUST00000068714	10	ENSMUSE00000140166	chr17:80833492-80832837	656	SOS1_MOUSE	401-620	220	0	-	-
1.11	ENSMUST00000068714	11	ENSMUSE00000458490	chr17:80823551-80823470	82	SOS1_MOUSE	620-647	28	0	-	-
1.12	ENSMUST00000068714	12	ENSMUSE00000140165	chr17:80822578-80822456	123	SOS1_MOUSE	647-688	42	0	-	-
1.13	ENSMUST00000068714	13	ENSMUSE00000251248	chr17:80822125-80822022	104	SOS1_MOUSE	688-723	36	0	-	-
1.14	ENSMUST00000068714	14	ENSMUSE00000140164	chr17:80819825-80819603	223	SOS1_MOUSE	723-797	75	0	-	-
1.15	ENSMUST00000068714	15	ENSMUSE00000140162	chr17:80818468-80818349	120	SOS1_MOUSE	797-837	41	0	-	-
1.16	ENSMUST00000068714	16	ENSMUSE00000140167	chr17:80814445-80814283	163	SOS1_MOUSE	837-891	55	0	-	-
1.17	ENSMUST00000068714	17	ENSMUSE00000140177	chr17:80813056-80812939	118	SOS1_MOUSE	892-931	40	0	-	-
1.18	ENSMUST00000068714	18	ENSMUSE00000539690	chr17:80808080-80807908	173	SOS1_MOUSE	931-988	58	0	-	-
1.19	ENSMUST00000068714	19	ENSMUSE00000140172	chr17:80807702-80807586	117	SOS1_MOUSE	989-1027	39	0	-	-
1.20	ENSMUST00000068714	20	ENSMUSE00000251076	chr17:80806298-80806031	268	SOS1_MOUSE	1028-1117	90	0	-	-
1.21	ENSMUST00000068714	21	ENSMUSE00000251053	chr17:80799199-80799081	119	SOS1_MOUSE	1117-1156	40	1	C:2-11 (gaps)	12
1.22	ENSMUST00000068714	22	ENSMUSE00000656958	chr17:80798012-80793092	4921	SOS1_MOUSE	1157-1319	163	0	-	-

Asymmetric/Biological Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:59
 aligned with CRK_MOUSE | Q64010 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:59
                                   142       152       162       172       182         
           CRK_MOUSE    133 EAEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYR  191
               SCOP domains d1b07a_ A: C-Crk, N-terminal SH3 domain                     SCOP domains
               CATH domains 1b07A00 A:133-191 SH3 Domains                               CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeee.....eeeee.....eeeeehhheee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                1b07 A  133 SAEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYH  191
                                   142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with SOS1_MOUSE | Q62245 from UniProtKB/Swiss-Prot  Length:1319

    Alignment length:12
                                  1141  
          SOS1_MOUSE   1132 EVPVPPPVPPRR 1143
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ....--...... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
               Transcript 1 Exon 1.21    Transcript 1
                1b07 C    2 EVPG--PVPPRR   11
                               |  |  9  
                               5  6

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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/Biological Unit

Classes(

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Folds(

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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: C-Crk, N-terminal SH3 domain (8)

Mouse (Mus musculus) [TaxId: 10090] (8)

d1b07a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

House mouse (Mus musculus) (29)

1b07A00

A:133-191

(no "Pfam Domain" information available for 1B07)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CRK_MOUSE | Q64010)

molecular function
	GO:0042169	SH2 domain binding	Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
	GO:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	GO:0046875	ephrin receptor binding	Interacting selectively and non-covalently with an ephrin receptor.
	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:0030674	protein binding, bridging	The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0045309	protein phosphorylated amino acid binding	Interacting selectively and non-covalently with a phosphorylated amino acid residue within a protein.
biological process
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0035020	regulation of Rac protein signal transduction	Any process that modulates the frequency, rate or extent of Rac protein signal transduction.
	GO:0032956	regulation of actin cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Chain C (SOS1_MOUSE | Q62245)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005089	Rho guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0001782	B cell homeostasis	The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0048514	blood vessel morphogenesis	The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
	GO:0003209	cardiac atrium morphogenesis	The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
	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:0061029	eyelid development in camera-type eye	The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye.
	GO:0001942	hair follicle development	The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
	GO:0003007	heart morphogenesis	The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0061384	heart trabecula morphogenesis	The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.
	GO:0002260	lymphocyte homeostasis	The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	GO:1904693	midbrain morphogenesis	The developmental process by which a midbrain is generated and organized.
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:0048011	neurotrophin TRK receptor signaling pathway	A series of molecular signals initiated by the binding of a neurotrophin 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.
	GO:0060021	palate development	The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
	GO:0003344	pericardium morphogenesis	The process in which the anatomical structure of the pericardium is generated and organized.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0045742	positive regulation of epidermal growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0051057	positive regulation of small GTPase mediated signal transduction	Any process that activates or increases the frequency, rate or extent of small GTPase mediated signal transduction.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
	GO:0033081	regulation of T cell differentiation in thymus	Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus.
	GO:0042129	regulation of T cell proliferation	Any process that modulates the frequency, rate or extent of T cell proliferation.
	GO:2000973	regulation of pro-B cell differentiation	Any process that modulates the frequency, rate or extent of pro-B cell differentiation.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
	GO:0007296	vitellogenesis	The production of yolk. Yolk is a mixture of materials used for embryonic nutrition.
cellular component
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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.
	GO:0014069	postsynaptic density of dendrite	An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1B07)

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