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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SRC HOMOLOGY-2 DOMAIN OF SH2-B IN COMPLEX WITH JAK2 PTYR813 PHOSPHOPEPTIDE
 
Authors :  J. Hu, S. R. Hubbard
Date :  21 Jun 06  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,G  (1x)
Biol. Unit 2:  B,H  (1x)
Biol. Unit 3:  C,I  (1x)
Biol. Unit 4:  D,J  (1x)
Biol. Unit 5:  E,K  (1x)
Biol. Unit 6:  F,L  (1x)
Keywords :  Sh2, Jak2, Phosphotyrosine, Adapter Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Hu, S. R. Hubbard
Structural Basis For Phosphotyrosine Recognition By The Src Homology-2 Domains Of The Adapter Proteins Sh2-B And Aps.
J. Mol. Biol. V. 361 69 2006
PubMed-ID: 16824542  |  Reference-DOI: 10.1016/J.JMB.2006.05.070
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SH2-B PH DOMAIN CONTAINING SIGNALING MEDIATOR 1 GAMMA ISOFORM
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSH2BPSM1
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - JAK2 PROTEIN
    ChainsG, H, I, J, K, L
    EngineeredYES
    Other DetailsSEQUENCE OCCURS NATURALLY IN MUS MUSCULUS (MOUSE).
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)A     G     
Biological Unit 2 (1x) B     H    
Biological Unit 3 (1x)  C     I   
Biological Unit 4 (1x)   D     J  
Biological Unit 5 (1x)    E     K 
Biological Unit 6 (1x)     F     L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1PTR6Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 2HDX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  6A:527-625
B:527-625
C:527-625
D:527-625
E:527-625
F:527-625
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  1A:527-625
-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  1-
B:527-625
-
-
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  1-
-
C:527-625
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  1-
-
-
D:527-625
-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  1-
-
-
-
E:527-625
-
Biological Unit 6 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B1_MOUSE527-625
 
 
 
 
 
  1-
-
-
-
-
F:527-625

(-) Exons   (0, 0)

(no "Exon" information available for 2HDX)

(-) 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:108
 aligned with SH2B1_MOUSE | Q91ZM2 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:108
                                   529       539       549       559       569       579       589       599       609       619        
          SH2B1_MOUSE   520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGEYVLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
               SCOP domains d2hdxa_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhhh.hhhhhh.eeeeee......eeeeeeee..eeeeeeeee.....eee..eee.hhhhhhhhhhhh...............ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------SH2  PDB: A:527-625 UniProt: 527-625                                                               -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2hdx A 520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGECVLTFNFQGKAKHLRLSLNAAGQCRVQHLHFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
                                   529       539       549       559       569       579       589       599       609       619        

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with SH2B1_MOUSE | Q91ZM2 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:108
                                   529       539       549       559       569       579       589       599       609       619        
          SH2B1_MOUSE   520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGEYVLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
               SCOP domains d2hdxb_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhhhhhhhhhh.eeeeee......eeeeeeee..eeeeeeeee.....eee..ee..hhhhhhhhhhhh......---......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------SH2  PDB: B:527-625 UniProt: 527-625                                                               -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2hdx B 520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGECVLTFNFQGKAKHLRLSLNAAGQCRVQHLHFQSIFDMLEHFRVHPIPLES---SDVVLVSYVPS 627
                                   529       539       549       559       569       579       589       599       609   |   619        
                                                                                                                       613 617          

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with SH2B1_MOUSE | Q91ZM2 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:108
                                   529       539       549       559       569       579       589       599       609       619        
          SH2B1_MOUSE   520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGEYVLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
               SCOP domains d2hdxc_ C: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhhhhhhhhhh..eeeee......eeeeeeee..eeeeeeeee.....eee..eee.hhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------SH2  PDB: C:527-625 UniProt: 527-625                                                               -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2hdx C 520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGECVLTFNFQGKAKHLRLSLNAAGQCRVQHLHFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
                                   529       539       549       559       569       579       589       599       609       619        

Chain D from PDB  Type:PROTEIN  Length:105
 aligned with SH2B1_MOUSE | Q91ZM2 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:108
                                   529       539       549       559       569       579       589       599       609       619        
          SH2B1_MOUSE   520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGEYVLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
               SCOP domains d2hdxd_ D: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhhhhhhhhhh.eeeeee......eeeeeeee..eeeeeeeee.....eee..eee.hhhhhhhhhhhh......---......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------SH2  PDB: D:527-625 UniProt: 527-625                                                               -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2hdx D 520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGECVLTFNFQGKAKHLRLSLNAAGQCRVQHLHFQSIFDMLEHFRVHPIPLES---SDVVLVSYVPS 627
                                   529       539       549       559       569       579       589       599       609   |   619        
                                                                                                                       613 617          

Chain E from PDB  Type:PROTEIN  Length:108
 aligned with SH2B1_MOUSE | Q91ZM2 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:108
                                   529       539       549       559       569       579       589       599       609       619        
          SH2B1_MOUSE   520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGEYVLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
               SCOP domains d2hdxe_ E: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhhhhhhhhhh.eeeeee......eeeeeeee..eeeeeeeee.....eee..eee.hhhhhhhhhhhh...............ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------SH2  PDB: E:527-625 UniProt: 527-625                                                               -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2hdx E 520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGECVLTFNFQGKAKHLRLSLNAAGQCRVQHLHFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
                                   529       539       549       559       569       579       589       599       609       619        

Chain F from PDB  Type:PROTEIN  Length:104
 aligned with SH2B1_MOUSE | Q91ZM2 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:108
                                   529       539       549       559       569       579       589       599       609       619        
          SH2B1_MOUSE   520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGEYVLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSYVPS 627
               SCOP domains d2hdxf_ F: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhhhhhhhhhh.eeeeee......eeeeeeee..eeeeeeeee.....eee..eee.hhhhhhhhhhhh......----.....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------SH2  PDB: F:527-625 UniProt: 527-625                                                               -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2hdx F 520 QPLSGYPWFHGMLSRLKAAQLVLEGGTGSHGVFLVRQSETRRGECVLTFNFQGKAKHLRLSLNAAGQCRVQHLHFQSIFDMLEHFRVHPIPLES----DVVLVSYVPS 627
                                   529       539       549       559       569       579       589       599       609   |   619        
                                                                                                                       613  618         

Chain G from PDB  Type:PROTEIN  Length:9
 aligned with JAK2_MOUSE | Q62120 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:9
           JAK2_MOUSE   810 TPDYELLTE 818
               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 --------- Transcript
                 2hdx G 810 TPDyELLTE 818
                               |     
                               |     
                             813-PTR 

Chain H from PDB  Type:PROTEIN  Length:7
 aligned with JAK2_MOUSE | Q62120 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:7
           JAK2_MOUSE   812 DYELLTE 818
               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 ------- Transcript
                 2hdx H 812 DyELLTE 818
                             |     
                             |     
                           813-PTR 

Chain I from PDB  Type:PROTEIN  Length:7
 aligned with JAK2_MOUSE | Q62120 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:7
           JAK2_MOUSE   812 DYELLTE 818
               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 ------- Transcript
                 2hdx I 812 DyELLTE 818
                             |     
                             |     
                           813-PTR 

Chain J from PDB  Type:PROTEIN  Length:7
 aligned with JAK2_MOUSE | Q62120 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:7
           JAK2_MOUSE   812 DYELLTE 818
               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 ------- Transcript
                 2hdx J 812 DyELLTE 818
                             |     
                             |     
                           813-PTR 

Chain K from PDB  Type:PROTEIN  Length:7
 aligned with JAK2_MOUSE | Q62120 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:7
           JAK2_MOUSE   812 DYELLTE 818
               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 ------- Transcript
                 2hdx K 812 DyELLTE 818
                             |     
                             |     
                           813-PTR 

Chain L from PDB  Type:PROTEIN  Length:9
 aligned with JAK2_MOUSE | Q62120 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:9
           JAK2_MOUSE   810 TPDYELLTE 818
               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 --------- Transcript
                 2hdx L 810 TPDyELLTE 818
                               |     
                             813-PTR 

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HDX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (112, 119)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (SH2B1_MOUSE | Q91ZM2)
molecular function
    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: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.
    GO:0035591    signaling adaptor activity    The binding activity of a molecule that brings together two or more molecules in a signaling pathway, permitting those molecules to function in a coordinated way. Adaptor molecules themselves do not have catalytic activity.
biological process
    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:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:2000278    regulation of DNA biosynthetic process    Any process that modulates the frequency, rate or extent of DNA biosynthetic process.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Chain G,H,I,J,K,L   (JAK2_MOUSE | Q62120)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0005131    growth hormone receptor binding    Interacting selectively and non-covalently with the growth hormone receptor.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0035401    histone kinase activity (H3-Y41 specific)    Catalysis of the transfer of a phosphate group to the tyrosine-41 residue of histone H3.
    GO:0005143    interleukin-12 receptor binding    Interacting selectively and non-covalently with the interleukin-12 receptor.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007259    JAK-STAT cascade    Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
    GO:0060397    JAK-STAT cascade involved in growth hormone signaling pathway    The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
    GO:0007262    STAT protein import into nucleus    The directed movement of dimerized STAT (Signal Transducers and Activators of Transcription) proteins into the nucleus following activation by members of the janus activated kinase (JAK) family of tyrosine kinases.
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0097296    activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0031103    axon regeneration    The regrowth of axons following their loss or damage.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0071549    cellular response to dexamethasone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dexamethasone stimulus.
    GO:0036016    cellular response to interleukin-3    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-3 stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007167    enzyme linked receptor protein signaling pathway    Any 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 catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0097191    extrinsic apoptotic signaling pathway    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
    GO:0060396    growth hormone receptor signaling pathway    The series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand.
    GO:0035409    histone H3-Y41 phosphorylation    The modification of histone H3 by the addition of a phosphate group to a tyrosine residue at position 41 of the histone.
    GO:0009755    hormone-mediated signaling pathway    A series of molecular signals mediated by the detection of a hormone.
    GO:0034050    host programmed cell death induced by symbiont    Cell death in a host resulting from activation of host endogenous cellular processes after direct or indirect interaction with a symbiont (defined as the smaller of two, or more, organisms engaged in symbiosis, a close interaction encompassing mutualism through parasitism). An example of direct interaction is contact with penetrating hyphae of a fungus; an example of indirect interaction is encountering symbiont-secreted molecules.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0035722    interleukin-12-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-12 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0008631    intrinsic apoptotic signaling pathway in response to oxidative stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered.
    GO:0061180    mammary gland epithelium development    The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
    GO:0031959    mineralocorticoid receptor signaling pathway    Any series of molecular signals generated as a consequence of a mineralocorticoid binding to its receptor.
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0022408    negative regulation of cell-cell adhesion    Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell.
    GO:0045822    negative regulation of heart contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
    GO:0050867    positive regulation of cell activation    Any process that activates or increases the frequency, rate or extent of activation.
    GO:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010811    positive regulation of cell-substrate adhesion    Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0060399    positive regulation of growth hormone receptor signaling pathway    Any process that increases the rate, frequency or extent of the growth hormone receptor signaling pathway. The growth hormone receptor signaling pathway is the series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0032024    positive regulation of insulin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
    GO:0032731    positive regulation of interleukin-1 beta production    Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production.
    GO:0045429    positive regulation of nitric oxide biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0051770    positive regulation of nitric-oxide synthase biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0032516    positive regulation of phosphoprotein phosphatase activity    Any process that activates or increases the activity of a phosphoprotein phosphatase.
    GO:0033160    positive regulation of protein import into nucleus, translocation    Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0035166    post-embryonic hemopoiesis    The stages of blood cell formation that take place after completion of embryonic development.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0060334    regulation of interferon-gamma-mediated signaling pathway    Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0097012    response to granulocyte macrophage colony-stimulating factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a granulocyte macrophage colony-stimulating factor stimulus.
    GO:0033194    response to hydroperoxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.
    GO:0070671    response to interleukin-12    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-12 stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0034612    response to tumor necrosis factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    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:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007260    tyrosine phosphorylation of STAT protein    The process of introducing a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
cellular component
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.

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