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- PDB-1prm: TWO BINDING ORIENTATIONS FOR PEPTIDES TO SRC SH3 DOMAIN: DEVELOPM... -

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Basic information

Entry
Database: PDB / ID: 1prm
TitleTWO BINDING ORIENTATIONS FOR PEPTIDES TO SRC SH3 DOMAIN: DEVELOPMENT OF A GENERAL MODEL FOR SH3-LIGAND INTERACTIONS
Components
  • C-SRC TYROSINE KINASE SH3 DOMAIN
  • PROLINE-RICH LIGAND PLR1 (AFAPPLPRR)
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / immune system process / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell-cell junction / cell junction / protein tyrosine kinase activity / protein phosphatase binding / cell differentiation / cytoskeleton / mitochondrial inner membrane / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily ...SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR
AuthorsFeng, S. / Chen, J.K. / Yu, H. / Simon, J.A. / Schreiber, S.L.
Citation
Journal: Science / Year: 1994
Title: Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions.
Authors: Feng, S. / Chen, J.K. / Yu, H. / Simon, J.A. / Schreiber, S.L.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Structural Basis for the Binding of Proline-Rich Peptides to SH3 Domains
Authors: Yu, H. / Chen, J.K. / Feng, S. / Dalgarno, D.C. / Brauer, A.W. / Schreiber, S.L.
#2: Journal: Science / Year: 1992
Title: Solution Structure of the SH3 Domain of Src and Identification of its Ligand-Binding Site
Authors: Yu, H. / Rosen, M.K. / Shin, T.B. / Seidel-Dugan, C. / Brugge, J.S. / Schreiber, S.L.
History
DepositionOct 10, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: C-SRC TYROSINE KINASE SH3 DOMAIN
A: PROLINE-RICH LIGAND PLR1 (AFAPPLPRR)


Theoretical massNumber of molelcules
Total (without water)8,0302
Polymers8,0302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein C-SRC TYROSINE KINASE SH3 DOMAIN


Mass: 7003.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SYNTHETIC OLIGO / Plasmid: PGEX-2T GENE: SYNTHETIC OLIGO / Production host: Escherichia coli (E. coli) / References: UniProt: P00523
#2: Protein/peptide PROLINE-RICH LIGAND PLR1 (AFAPPLPRR)


Mass: 1026.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 1

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