Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  NMR STRUCTURE OF THE N-TERMINAL SH3 DOMAIN OF DRK (CALCULATED WITHOUT NOE RESTRAINTS)
 
Authors :  I. Bezsonova, A. U. Singer, W. -Y. Choy, M. Tollinger, J. D. Forman-Kay
Date :  12 Sep 05  (Deposition) - 13 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Drosophila Melanogaster, Sh3 Fragment, Drk, Nmr Structure, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Bezsonova, A. Singer, W. -Y. Choy, M. Tollinger, J. D. Forman-Kay
Structural Comparison Of The Unstable Drkn Sh3 Domain And A Stable Mutant
Biochemistry V. 44 15550 2005
PubMed-ID: 16300404  |  Reference-DOI: 10.1021/BI0512795
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SH2-SH3 ADAPTER PROTEIN DRK
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-11A
    Expression System StrainHMS174
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL SH3 DOMAIN, RESIDUES 1-59
    GeneDRK, E SEV 2B
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymPROTEIN ENHANCER OF SEVENLESS 2B, DOWNSTREAM OF RECEPTOR KINASE, PROTEIN ESEV 2B

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AZS)

(-) Sites  (0, 0)

(no "Site" information available for 2AZS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AZS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AZS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AZS)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.DRK_DROME1-58
152-211
  1A:1-58
-

(-) Exons   (0, 0)

(no "Exon" information available for 2AZS)

(-) Sequences/Alignments

NMR Structure
   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
(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:59
 aligned with DRK_DROME | Q08012 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:59
                                    10        20        30        40        50         
             DRK_DROME    1 MEAIAKHDFSATADDELSFRKTQILKILNMEDDSNWYRAELDGKEGLIPSNYIEMKNHD 59
               SCOP domains d2azsa_ A: automated matches                                SCOP domains
               CATH domains 2azsA00 A:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.................eeeeeee......eeeeee..eeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE SH3  PDB: A:1-58 UniProt: 1-58                            - PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  2azs A  1 MEAIAKHDFSATADDELSFRKTQILKILNMEDDSNWYRAELDGKEGLIPSNYIEMKNHD 59
                                    10        20        30        40        50         

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AZS)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (DRK_DROME | Q08012)
molecular function
    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: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:0005118    sevenless binding    Interacting selectively and non-covalently with the sevenless (sev) protein, a receptor tyrosine kinase.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    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:0038202    TORC1 signaling    A series of intracellular molecular signals mediated by TORC1; TOR (target of rapamycin) in complex with at least Raptor (regulatory-associated protein of TOR), or orthologs of, and other signaling components.
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0007256    activation of JNKK activity    The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress.
    GO:0008595    anterior/posterior axis specification, embryo    The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote.
    GO:0008306    associative learning    Learning by associating a stimulus (the cause) with a particular outcome (the effect).
    GO:0001700    embryonic development via the syncytial blastoderm    The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0007175    negative regulation of epidermal growth factor-activated receptor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity.
    GO:0008355    olfactory learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue.
    GO:0030707    ovarian follicle cell development    The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. An example of this is found in Drosophila melanogaster.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0045678    positive regulation of R7 cell differentiation    Any process that activates or increases the frequency, rate or extent of R7 cell differentiation.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0045500    sevenless signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to sevenless (sev; a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007614    short-term memory    The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0008293    torso signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2azs)
 
  Sites
(no "Sites" information available for 2azs)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2azs)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2azs
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DRK_DROME | Q08012
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DRK_DROME | Q08012
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DRK_DROME | Q080122a36 2a37 2azv

(-) Related Entries Specified in the PDB File

5923 CO, N AND HN CHEMICAL SHIFTS OF THE T22G MUTANT OF THE N- TERMINAL SH3 DOMAIN OF DRK
5925 CO, N AND HN CHEMICAL SHIFTS OF THE N-TERMINAL SH3 DOMAIN OF DRK
2a36 SOLUTION STRUCTURE OF THE N-TERMINAL SH3 DOMAIN OF DRK (CALCULATED WITH NOE RESTRAINTS)
2a37 SOLUTION STRUCTURE OF THE T22G MUTANT OF THE N-TERMINAL SH3 DOMAIN OF DRK (CALCULATED WITH NOE RESTRAINTS)
2azv SOLUTION STRUCTURE OF THE T22G MUTANT OF N-TERMINAL SH3 DOMAIN OF DRK (CALCULATED WITHOUT NOES)