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(-) Description

Title :  CRYSTAL STRUCTURE OF JNK2
 
Authors :  A. Kuglstatter, A. G. Villasenor
Date :  18 Aug 08  (Deposition) - 09 Sep 08  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Map Kinase Insert, Activation Loop, Indazole Inhibitor, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Shaw, S. M. Wang, A. G. Villasenor, S. Tsing, D. Walter, M. F. Browner J. Barnett, A. Kuglstatter
The Crystal Structure Of Jnk2 Reveals Conformational Flexibility In The Map Kinase Insert And Indicates Its Involvement In The Regulation Of Catalytic Activity.
J. Mol. Biol. V. 383 885 2008
PubMed-ID: 18801372  |  Reference-DOI: 10.1016/J.JMB.2008.08.086

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 9
    ChainsA, B
    EC Number2.7.11.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 7-362
    GeneMAPK9, JNK2, PRKM9
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTRESS-ACTIVATED PROTEIN KINASE JNK2, C-JUN N-TERMINAL KINASE 2, JNK-55

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A (1x)B (1x)
Biological Unit 2 (1x)A 
Biological Unit 3 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
135F2Ligand/IonN-{3-[5-(1H-1,2,4-TRIAZOL-3-YL)-1H-INDAZOL-3-YL]PHENYL}FURAN-2-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
135F1Ligand/IonN-{3-[5-(1H-1,2,4-TRIAZOL-3-YL)-1H-INDAZOL-3-YL]PHENYL}FURAN-2-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
135F1Ligand/IonN-{3-[5-(1H-1,2,4-TRIAZOL-3-YL)-1H-INDAZOL-3-YL]PHENYL}FURAN-2-CARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
135F1Ligand/IonN-{3-[5-(1H-1,2,4-TRIAZOL-3-YL)-1H-INDAZOL-3-YL]PHENYL}FURAN-2-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:53 , GLU A:109 , LEU A:110 , MET A:111 , ASP A:112 , ALA A:113 , ASN A:114 , LEU A:168 , HOH A:454 , LYS B:30 , ASN B:51 , LEU B:110BINDING SITE FOR RESIDUE 35F A 1
2AC2SOFTWARELYS A:30 , ASN A:51 , GLU B:109 , MET B:111 , ASP B:112 , ALA B:113 , HOH B:555BINDING SITE FOR RESIDUE 35F B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E7O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E7O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042260V13MMK09_HUMANUnclassified  ---A/BV13M
2UniProtVAR_042261K56NMK09_HUMANUnclassified  ---A/BK56N
3UniProtVAR_042262A246TMK09_HUMANPolymorphism35421153A/BA246T
4UniProtVAR_025175G268AMK09_HUMANPolymorphism35693958A/BG268A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042260V13MMK09_HUMANUnclassified  ---A/BV13M
2UniProtVAR_042261K56NMK09_HUMANUnclassified  ---A/BK56N
3UniProtVAR_042262A246TMK09_HUMANPolymorphism35421153A/BA246T
4UniProtVAR_025175G268AMK09_HUMANPolymorphism35693958A/BG268A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042260V13MMK09_HUMANUnclassified  ---AV13M
2UniProtVAR_042261K56NMK09_HUMANUnclassified  ---AK56N
3UniProtVAR_042262A246TMK09_HUMANPolymorphism35421153AA246T
4UniProtVAR_025175G268AMK09_HUMANPolymorphism35693958AG268A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042260V13MMK09_HUMANUnclassified  ---BV13M
2UniProtVAR_042261K56NMK09_HUMANUnclassified  ---BK56N
3UniProtVAR_042262A246TMK09_HUMANPolymorphism35421153BA246T
4UniProtVAR_025175G268AMK09_HUMANPolymorphism35693958BG268A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAPKPS01351 MAP kinase signature.MK09_HUMAN61-163
 
  2A:61-163
B:61-163
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK09_HUMAN147-159
 
  2A:147-159
B:147-159
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAPKPS01351 MAP kinase signature.MK09_HUMAN61-163
 
  2A:61-163
B:61-163
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK09_HUMAN147-159
 
  2A:147-159
B:147-159
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAPKPS01351 MAP kinase signature.MK09_HUMAN61-163
 
  1A:61-163
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK09_HUMAN147-159
 
  1A:147-159
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAPKPS01351 MAP kinase signature.MK09_HUMAN61-163
 
  1-
B:61-163
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK09_HUMAN147-159
 
  1-
B:147-159

(-) Exons   (0, 0)

(no "Exon" information available for 3E7O)

(-) 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:342
 aligned with MK09_HUMAN | P45984 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:353
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
           MK09_HUMAN     9 QFYSVQVADSTFTVLKRYQQLKPIGSGAQGIVCAAFDTVLGINVAVKKLSRPFQNQTHAKRAYRELVLLKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIHMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTACTNFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGELVKGCVIFQGTDHIDQWNKVIEQLGTPSAEFMKKLQPTVRNYVENRPKYPGIKFEELFPDWIFPSESERDKIKTSQARDLLSKMLVIDPDKRISVDEALRHPYITVWYDPAEAEAPPPQIYDAQLEEREHAIEEWKELIYKEVM 361
               SCOP domains d3e7oa_ A: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -3e7oA01 A:10-112 Phosphorylase Kinase; domain 1                                                        3e7oA02 A:113-332 Transferase(Phosphotransferase) domain 1                                                                                                                                                                  -----         --------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee..eeeeeeee....eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee............eeeee...eehhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........................hhhhhh......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhh.hhhhhhhhhh.......hhhhhhhhhhh.--.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..............---------.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----M------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------------A--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------MAPK  PDB: A:61-163 UniProt: 61-163                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e7o A   9 QFYSVQVADSTFTVLKRYQQLKPIGSGAQGIVCAAFDTVLGINVAVKKLSRPFQNQTHAKRAYRELVLLKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIHMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTASTNFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGELVKGSVIFQGTDHIDQWNKVIEQLGTPSAEFMAALQPTVRNYVENRPAYPGIAFEELFPDWIFP--SERDKIKTSQARDLLSKMLVIDPDKRISVDEALRHPYITVWYDPAEAEAPPPQI---------HAIEEWKELIYKEVM 361
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278  |  | 288       298       308       318       328        |-       348       358   
                                                                                                                                                                                                                                                                                                          281  |                                                  337       347              
                                                                                                                                                                                                                                                                                                             284                                                                             

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with MK09_HUMAN | P45984 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:355
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     
           MK09_HUMAN     8 SQFYSVQVADSTFTVLKRYQQLKPIGSGAQGIVCAAFDTVLGINVAVKKLSRPFQNQTHAKRAYRELVLLKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIHMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTACTNFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGELVKGCVIFQGTDHIDQWNKVIEQLGTPSAEFMKKLQPTVRNYVENRPKYPGIKFEELFPDWIFPSESERDKIKTSQARDLLSKMLVIDPDKRISVDEALRHPYITVWYDPAEAEAPPPQIYDAQLEEREHAIEEWKELIYKEVMD 362
               SCOP domains d3e7ob_ B: automated matche   s                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --3e7oB01 B:10-112 Phosphor   ylase Kinase; domain 1                                                     3e7oB02 B:113-332 Transferase(Phosphotransferase) domain 1                                                                                                                                                                  -----       ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee..eeeeeeee.---.eeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhh.......eeeee............eeeee...eehhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....----------------hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhh..hhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhh..hhhhh...---......-------...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----M------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------------A---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------MAPK  PDB: B:61-163 UniProt: 61-163                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e7o B   8 SQFYSVQVADSTFTVLKRYQQLKPIGS---GIVCAAFDTVLGINVAVKKLSRPFQNQTHAKRAYRELVLLKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIHMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFG----------------TRYYRAPEVILGMGYKENVDIWSVGCIMGELVKGSVIFQGTDHIDQWNKVIEQLGTPSAEFMAALQPTVRNYVENRPAYPGIAFEELFPDWIFPSESERDKIKTSQARDLLSKMLVIDPDKRISVDEALRHPYITVWYDPA---APPPQI-------REHAIEEWKELIYKEVMD 362
                                    17        27      |  -|       47        57        67        77        87        97       107       117       127       137       147       157       167   |     -         -|      197       207       217       227       237       247       257       267       277       287       297       307       317       327|   |  337       347       357     
                                                     34  38                                                                                                                                  171              188                                                                                                                                         328 332  337     345                 

   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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E7O)

(-) Gene Ontology  (58, 58)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MK09_HUMAN | P45984)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004705    JUN kinase activity    Catalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors.
    GO:0004707    MAP kinase activity    Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.
    GO:0008656    cysteine-type endopeptidase activator activity involved in apoptotic process    Increases the rate of proteolysis catalyzed by a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0031435    mitogen-activated protein kinase kinase kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase.
    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:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (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:0007258    JUN phosphorylation    The process of introducing a phosphate group into a JUN protein.
    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:0034644    cellular response to UV    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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0071363    cellular response to growth factor 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 growth factor stimulus.
    GO:0071347    cellular response to interleukin-1    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-1 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:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
    GO:0010770    positive regulation of cell morphogenesis involved in differentiation    Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized 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.
    GO:0032722    positive regulation of chemokine production    Any process that activates or increases the frequency, rate, or extent of chemokine production.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0010744    positive regulation of macrophage derived foam cell differentiation    Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    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:0071803    positive regulation of podosome assembly    Any process that activates or increases the rate or extent of podosome assembly.
    GO:0031394    positive regulation of prostaglandin biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of prostaglandin.
    GO:0032308    positive regulation of prostaglandin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of a prostaglandin from a cell.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0046328    regulation of JNK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0031396    regulation of protein ubiquitination    Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0051090    regulation of sequence-specific DNA binding transcription factor activity    Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0001836    release of cytochrome c from mitochondria    The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
    GO:0014075    response to amine    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 amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    GO:0046686    response to cadmium ion    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 cadmium (Cd) ion stimulus.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0009612    response to mechanical stimulus    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 mechanical stimulus.
    GO:0010033    response to organic substance    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 organic substance stimulus.
    GO:0006950    response to 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 a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0009636    response to toxic substance    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 toxic stimulus.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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