Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF DOK1 PTB DOMAIN
 
Authors :  N. Shi, S. Ye, Y. Liu, W. Zhou, Y. Ding, Z. Lou, B. Qiang, J. Yuan, Z. Rao
Date :  28 Apr 03  (Deposition) - 17 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shi, S. Ye, M. Bartlam, M. Yang, J. Wu, Y. Liu, F. Sun, X. Han, X. Peng, B. Qiang, J. Yuan, Z. Rao
Structural Basis For The Specific Recognition Of Ret By The Dok1 Phosphotyrosine Binding Domain
J. Biol. Chem. V. 279 4962 2004
PubMed-ID: 14607833  |  Reference-DOI: 10.1074/JBC.M311030200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOCKING PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: DOK1 PTB DOMAIN
    Gene: MDOK1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DOK1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1P5T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P5T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P5T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P5T)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRS_PTBPS51064 IRS-type PTB domain profile.DOK1_MOUSE151-259
 		  2A:5-110
B:5-108

(-) Exons   (0, 0)

(no "Exon" information available for 1P5T)

(-) Sequences/Alignments

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
(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:107
 aligned with DOK1_MOUSE | P97465 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:107
                                   160       170       180       190       200       210       220       230       240       250       
           DOK1_MOUSE   151 EGSQFWVTSQKTEASERCGLQGSYILRVEAEKLTLLTLGAQSQILEPLLFWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTSQGNDIFQAVEAAIQQQKAQGK 257
               SCOP domains d1p5ta_ A: Docking protein 1, Dok1                                                                          SCOP domains
               CATH domains -1p5tA00 A:5-110 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhh....eeeeee...eeeeeee......eeeeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE IRS_PTB  PDB: A:5-110 UniProt: 151-259                                                                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1p5t A   4 mGSQFWVTSQKTEASERCGLQGSYILRVEAEKLTLLTLGAQSQILEPLLFWPYTLLRRYGRDKVmFSFEAGRRCPSGPGTFTFQTSQGNDIFQAVEAAIQQQKAQGK 110
                            |       13        23        33        43        53        63    |   73        83        93       103       
                            |                                                              68-MSE                                      
                            4-MSE                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with DOK1_MOUSE | P97465 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:105
                                   160       170       180       190       200       210       220       230       240       250     
           DOK1_MOUSE   151 EGSQFWVTSQKTEASERCGLQGSYILRVEAEKLTLLTLGAQSQILEPLLFWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTSQGNDIFQAVEAAIQQQKAQ 255
               SCOP domains d1p5tb_ B: Docking protein 1, Dok1                                                                        SCOP domains
               CATH domains -1p5tB00 B:5-108 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)              CATH domains
           Pfam domains (1) -IRS-1p5tB01 B:5-107                                                                                    - Pfam domains (1)
           Pfam domains (2) -IRS-1p5tB02 B:5-107                                                                                    - Pfam domains (2)
         Sec.struct. author ..eeeeeee..hhhhhhh....eeeeee...eeeeeee......eeeeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE IRS_PTB  PDB: B:5-108 UniProt: 151-259                                                                    PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1p5t B   4 mGSQFWVTSQKTEASERCGLQGSYILRVEAEKLTLLTLGAQSQILEPLLFWPYTLLRRYGRDKVmFSFEAGRRCPSGPGTFTFQTSQGNDIFQAVEAAIQQQKAQ 108
                            |       13        23        33        43        53        63    |   73        83        93       103     
                            4-MSE                                                          68-MSE
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: IRS] (14)
(-)
Family: IRS (14)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DOK1_MOUSE | P97465)
molecular function
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin 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:0005057    signal transducer activity, downstream of receptor    Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    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:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1p5t)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1p5t)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1p5t
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DOK1_MOUSE | P97465
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DOK1_MOUSE | P97465
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DOK1_MOUSE | P97465: 1uef

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1P5T)