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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE DOK-5 PTB DOMAIN
 
Authors :  N. Shi, Y. Ding, B. Q. Qiang, J. G. Yuan, Z. H. Rao
Date :  25 Nov 02  (Deposition) - 16 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Strands, Alfa Helix, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shi, Y. Ding, B. Q. Qiang, J. G. Yuan, Z. H. Rao
Crystal Structure Analysis Of The Dok-5 Ptb Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOWNSTREAM OF TYROSINE KINASE 5
    Chains: A, B
    EC Number: 2.7.1.112
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DOK5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOK-5 PTB DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1J0W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J0W)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002625931aENSE00001921899chr20:53092136-53092551416DOK5_HUMAN1-22220--
1.3ENST000002625933ENSE00001596017chr20:53171472-53171579108DOK5_HUMAN23-58360--
1.5ENST000002625935ENSE00001636084chr20:53205022-53205136115DOK5_HUMAN59-97390--
1.6ENST000002625936ENSE00001718492chr20:53205226-53205345120DOK5_HUMAN97-137412A:9-11
B:7-11		3
5
1.7ENST000002625937ENSE00000662863chr20:53208155-53208344190DOK5_HUMAN137-200642A:11-74
B:11-74		64
64
1.8ENST000002625938ENSE00000845676chr20:53226927-53227062136DOK5_HUMAN200-245462A:74-107
B:74-109 (gaps)		34
37
1.9ENST000002625939ENSE00000845677chr20:53259997-53260117121DOK5_HUMAN246-286410--
1.10bENST0000026259310bENSE00001455163chr20:53266954-53267710757DOK5_HUMAN286-306210--

(-) Sequences/Alignments

Asymmetric 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:99
 aligned with DOK5_HUMAN | Q9P104 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:99
                                   144       154       164       174       184       194       204       214       224         
           DOK5_HUMAN   135 QSERFNVYLMPSPNLDVHGECALQITYEYICLWDVQNPRVKLISWPLSALRRYGRDTTWFTFEAGRMCETGEGLFIFQTRDGEAIYQKVHSAALAIAEQ 233
               SCOP domains d1j0wa_ A: Downstream of tyrosine kinase 5, Dok-5                                                   SCOP domains
               CATH domains 1j0wA00 A:9-107 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeee...eeeeee......eeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.6--------------------------------------------------------------Exon 1.8  PDB: A:74-107            Transcript 1 (1)
           Transcript 1 (2) --Exon 1.7  PDB: A:11-74 UniProt: 137-200                         --------------------------------- Transcript 1 (2)
                 1j0w A   9 QSERFNVYLmPSPNLDVHGECALQITYEYICLWDVQNPRVKLISWPLSALRRYGRDTTWFTFEAGRmCETGEGLFIFQTRDGEAIYQKVHSAALAIAEL 107
                                    18        28        38        48        58        68      | 78        88        98         
                                    18-MSE                                                   75-MSE                            


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with DOK5_HUMAN | Q9P104 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:104
                                   142       152       162       172       182       192       202       212       222       232    
           DOK5_HUMAN   133 REQSERFNVYLMPSPNLDVHGECALQITYEYICLWDVQNPRVKLISWPLSALRRYGRDTTWFTFEAGRMCETGEGLFIFQTRDGEAIYQKVHSAALAIAEQHER 236
               SCOP domains d1j0wb_ B: Downstream of tyrosine kinase 5, Dok-5                                                        SCOP domains
               CATH domains 1j0wB00 B:7-109 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.........eeeeeee...eeeee.......eeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhhhhh-hh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.6  --------------------------------------------------------------Exon 1.8  PDB: B:74-109 (gaps)        Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.7  PDB: B:11-74 UniProt: 137-200                         ------------------------------------ Transcript 1 (2)
                 1j0w B   7 REQSERFNVYLmPSPNLDVHGECALQITYEYICLWDVQNPRVKLISWPLSALRRYGRDTTWFTFEAGRmCETGEGLFIFQTRDGEAIYQKVHSAALAIAEL-ER 109
                                    16 |      26        36        46        56        66        76        86        96       106| | 
                                      18-MSE                                                   75-MSE                         107 | 
                                                                                                                                108
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J0W)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DOK5_HUMAN | Q9P104)
molecular function
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0051386    regulation of neurotrophin TRK receptor signaling pathway    Any process that modulates the frequency, rate or extent of the neurotrophin TRK receptor signaling pathway.
    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: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.

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  1j0w
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