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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOGEN ACTIVATED PROTEIN KINASE 11 (P38 BETA) IN COMPLEX WITH NILOTINIB
 
Authors :  P. Filippakopoulos, A. Barr, O. Fedorov, T. Keates, M. Soundararajan, E. Salah, N. Burgess-Brown, E. Ugochukwu, A. C. W. Pike, J. Muniz, A. Ro A. Chaikuad, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)
Date :  20 Mar 09  (Deposition) - 07 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Mitogen-Activated Protein Kinase 11, P38B, P38Beta, Prkm11, Sapk2, Sapk2B, Stress-Activated Protein Kinase-2, Structural Genomics Consortium, Sgc, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, A. Barr, O. Fedorov, T. Keates, M. Soundararajan J. Elkins, E. Salah, N. Burgess-Brown, E. Ugochukwu, A. C. W. Pike, J. Muniz, A. Roos, A. Chaikuad, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Mitogen Activated Protein Kinase 11 (P38 Beta) In Complex With Nilotinib
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 11
    ChainsA
    EC Number2.7.11.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAPK11, PRKM11, SAPK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAPK11, MITOGEN-ACTIVATED PROTEIN KINASE P38 BETA, MAP KINASE P38 BETA, P38B, P38-2, STRESS-ACTIVATED PROTEIN KINASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NIL1Ligand/IonNILOTINIB

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:51 , LYS A:53 , ARG A:67 , GLU A:71 , VAL A:83 , ILE A:84 , THR A:106 , MET A:109 , HIS A:148 , LEU A:167 , ASP A:168 , PHE A:169 , HOH A:441BINDING SITE FOR RESIDUE NIL A 1
2AC2SOFTWAREGLN A:22 , GLN A:25 , ARG A:73 , ASP A:324 , HOH A:390 , HOH A:518BINDING SITE FOR RESIDUE EDO A 351
3AC3SOFTWAREARG A:23 , ARG A:45 , ASP A:88 , HOH A:542BINDING SITE FOR RESIDUE CL A 352

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GP0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:30 -Gly A:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042264A221VMK11_HUMANUnclassified  ---AA221V
2UniProtVAR_025176R275HMK11_HUMANPolymorphism33932986AR275H

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK11_HUMAN30-54  1A:30-54
2MAPKPS01351 MAP kinase signature.MK11_HUMAN59-162  1A:59-162

(-) Exons   (0, 0)

(no "Exon" information available for 3GP0)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:333
 aligned with MK11_HUMAN | Q15759 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:345
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343     
           MK11_HUMAN     4 PRAGFYRQELNKTVWEVPQRLQGLRPVGSGAYGSVCSAYDARLRQKVAVKKLSRPFQSLIHARRTYRELRLLKHLKHENVIGLLDVFTPATSIEDFSEVYLVTTLMGADLNNIVKCQALSDEHVQFLVYQLLRGLKYIHSAGIIHRDLKPSNVAVNEDCELRILDFGLARQADEEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLQGKALFPGSDYIDQLKRIMEVVGTPSPEVLAKISSEHARTYIQSLPPMPQKDLSSIFRGANPLAIDLLGRMLVLDSDQRVSAAEALAHAYFSQYHDPEDEPEAEPYDESVEAKERTLEEWKELTYQEVLSF 348
               SCOP domains d3gp0a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -3gp0A01 A:5-110,A:320-348 P     hosphorylase Kinase; domain 1                                             3gp0A02 A:111-319 Transferase(Phosphotransferase) domain 1                                                                                                                                                       3gp0A01 A:5-110,A:320-348     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeee..eeeeee..-----.eeeeee....eeeeeee......hhhhhhhhhhhhhhhhhh.......eeeee....hhhhh...eeeee...eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....------...-...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh....hhhhhhh.......hhhhhh...hhhhhhhhh.....hhhhh.hhhhhhhhhhhh...hhhhh.......hhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------------------------------H------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------PROTEIN_KINASE_ATP       ----MAPK  PDB: A:59-162 UniProt: 59-162                                                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gp0 A   4 MRAGFYRQELNKTVWEVPQRLQGLRPVG-----SVCSAYDARLRQKVAVKKLSRPFQSLIHARRTYRELRLLKHLKHENVIGLLDVFTPATSIEDFSEVYLVTTLMGADLNNIVKCQALSDEHVQFLVYQLLRGLKYIHSAGIIHRDLKPSNVAVNEDCELRILDFG------EEM-GYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLQGKALFPGSDYIDQLKRIMEVVGTPSPEVLAKISSEHARTYIQSLPPMPQKDLSSIFRGANPLAIDLLGRMLVLDSDQRVSAAEALAHAYFSQYHDPEDEPEAEPYDESVEAKERTLEEWKELTYQEVLSF 348
                                    13        23       | -   |    43        53        63        73        83        93       103       113       123       133       143       153       163      |  -   | | 183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343     
                                                      31    37                                                                                                                                  170    177 | |                                                                                                                                                                       
                                                                                                                                                                                                         179 |                                                                                                                                                                       
                                                                                                                                                                                                           181                                                                                                                                                                       

   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/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GP0)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MK11_HUMAN | Q15759)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0098586    cellular response to virus    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 stimulus from a virus.
    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:0060044    negative regulation of cardiac muscle cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation.
    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:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    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:2001184    positive regulation of interleukin-12 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-12 secretion.
    GO:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0060043    regulation of cardiac muscle cell proliferation    Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation.
    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:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        MK11_HUMAN | Q157593gc8 3gc9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GP0)