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(-) Description

Title :  PKC ETA KINASE IN COMPLEX WITH A NAPHTHYRIDINE
 
Authors :  W. Stark, G. Rummel, S. W. Cowan-Jacob
Date :  23 Sep 11  (Deposition) - 30 Nov 11  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Kinase, Phosphotransferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Van Eis, J. P. Evenou, P. Floersheim, C. Gaul, S. W. Cowan-Jacob, L. Monovich, G. Rummel, W. Schuler, W. Stark, A. Strauss, A. Matt, E. Vangrevelinghe, J. Wagner, N. Soldermann
2, 6-Naphthyridines As Potent And Selective Inhibitors Of Th Novel Protein Kinase C Isozymes.
Bioorg. Med. Chem. Lett. V. 21 7367 2011
PubMed-ID: 22078216  |  Reference-DOI: 10.1016/J.BMCL.2011.10.025

(-) Compounds

Molecule 1 - PROTEIN KINASE C ETA TYPE
    ChainsA
    EC Number2.7.11.13
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    FragmentKINASE DOMAIN, RESIDUES 333-683
    GenePRKCH, PKCL, PRKCL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPKC-L, NPKC-ETA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
107U1Ligand/Ion2-METHYL-N~1~-[3-(PYRIDIN-4-YL)-2,6-NAPHTHYRIDIN-1-YL]PROPANE-1,2-DIAMINE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
107U1Ligand/Ion2-METHYL-N~1~-[3-(PYRIDIN-4-YL)-2,6-NAPHTHYRIDIN-1-YL]PROPANE-1,2-DIAMINE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
107U2Ligand/Ion2-METHYL-N~1~-[3-(PYRIDIN-4-YL)-2,6-NAPHTHYRIDIN-1-YL]PROPANE-1,2-DIAMINE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:366 , VAL A:369 , ALA A:382 , LYS A:384 , GLU A:434 , VAL A:436 , ASP A:440 , ASP A:483 , LEU A:486 , ASP A:497BINDING SITE FOR RESIDUE 07U A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042315R359QKPCL_HUMANPolymorphism55818778AR359Q
2UniProtVAR_034604V374IKPCL_HUMANPolymorphism2230500AV374I
3UniProtVAR_060736D497YKPCL_HUMANPolymorphism11846991AD497Y
4UniProtVAR_042316T575AKPCL_HUMANUnclassified  ---AT575A
5UniProtVAR_042317T594IKPCL_HUMANUnclassified  ---AT594I
6UniProtVAR_042318P612SKPCL_HUMANPolymorphism34159231AP612S
7UniProtVAR_042438D645VKPCL_HUMANPolymorphism35561533AD645V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042315R359QKPCL_HUMANPolymorphism55818778AR359Q
2UniProtVAR_034604V374IKPCL_HUMANPolymorphism2230500AV374I
3UniProtVAR_060736D497YKPCL_HUMANPolymorphism11846991AD497Y
4UniProtVAR_042316T575AKPCL_HUMANUnclassified  ---AT575A
5UniProtVAR_042317T594IKPCL_HUMANUnclassified  ---AT594I
6UniProtVAR_042318P612SKPCL_HUMANPolymorphism34159231AP612S
7UniProtVAR_042438D645VKPCL_HUMANPolymorphism35561533AD645V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (7, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042315R359QKPCL_HUMANPolymorphism55818778AR359Q
2UniProtVAR_034604V374IKPCL_HUMANPolymorphism2230500AV374I
3UniProtVAR_060736D497YKPCL_HUMANPolymorphism11846991AD497Y
4UniProtVAR_042316T575AKPCL_HUMANUnclassified  ---AT575A
5UniProtVAR_042317T594IKPCL_HUMANUnclassified  ---AT594I
6UniProtVAR_042318P612SKPCL_HUMANPolymorphism34159231AP612S
7UniProtVAR_042438D645VKPCL_HUMANPolymorphism35561533AD645V

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KPCL_HUMAN361-384  1A:361-384
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KPCL_HUMAN475-487  1A:475-487
3AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.KPCL_HUMAN615-683  1A:615-679
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KPCL_HUMAN361-384  1A:361-384
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KPCL_HUMAN475-487  1A:475-487
3AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.KPCL_HUMAN615-683  1A:615-679
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KPCL_HUMAN361-384  2A:361-384
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KPCL_HUMAN475-487  2A:475-487
3AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.KPCL_HUMAN615-683  2A:615-679

(-) Exons   (0, 0)

(no "Exon" information available for 3TXO)

(-) 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:318
 aligned with KPCL_HUMAN | P24723 from UniProtKB/Swiss-Prot  Length:683

    Alignment length:327
                                   362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       
           KPCL_HUMAN   353 DNFEFIRVLGKGSFGKVMLARVKETGDLYAVKVLKKDVILQDDDVECTMTEKRILSLARNHPFLTQLFCCFQTPDRLFFVMEFVNGGDLMFHIQKSRRFDEARARFYAAEIISALMFLHDKGIIYRDLKLDNVLLDHEGHCKLADFGMCKEGICNGVTTATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAILNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQIEPPFRPRIKSREDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFRNFSYVSP 679
               SCOP domains d3txoa_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhh........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...........---------.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhh....................hhhhhh...........hhhhhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------Q--------------I--------------------------------------------------------------------------------------------------------------------------Y-----------------------------------------------------------------------------A------------------I-----------------S--------------------------------V---------------------------------- SAPs(SNPs)
                    PROSITE --------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: A:615-679 UniProt: 615-683                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3txo A 353 DNFEFIRVLGKGSFGKVMLARVKETGDLYAVKVLKKDVILQDDDVECTMTEKRILSLARNHPFLTQLFCCFQTPDRLFFVMEFVNGGDLMFHIQKSRRFDEARARFYAAEIISALMFLHDKGIIYRDLKLDNVLLDHEGHCKLADFGMCKEGIC---------GTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAILNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQIEPPFRPRIKSREDVSNFDPDFIKEEPVLtPIDEGHLPMINQDEFRNFEYVSP 679
                                   362       372       382       392       402       412       422       432       442       452       462       472       482       492       502   |     -   |   522       532       542       552       562       572       582       592       602       612       622       632       642       652   |   662       672       
                                                                                                                                                                                   506       516                                                                                                                                         656-TPO                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TXO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A   (KPCL_HUMAN | P24723)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0017160    Ral GTPase binding    Interacting selectively and non-covalently with Ral protein, any member of the Ral subfamily of the Ras superfamily of monomeric GTPases.
    GO:0004699    calcium-independent protein kinase C activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol but not calcium.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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: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:0004697    protein kinase C activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol.
    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: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: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: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:0034351    negative regulation of glial cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0050861    positive regulation of B cell receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0060252    positive regulation of glial cell proliferation    Any process that activates or increases the rate or extent of glial cell proliferation.
    GO:0045618    positive regulation of keratinocyte differentiation    Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation.
    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:0070528    protein kinase C signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:2000810    regulation of bicellular tight junction assembly    Any process that modulates the frequency, rate or extent of tight junction assembly.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        KPCL_HUMAN | P247232fk9

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