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(-) Description

Title :  CRYSTAL STRUCTURE OF MNK2-D228G IN COMPLEX WITH STAUROSPORINE
 
Authors :  R. Jauch, M. C. Wahl
Date :  01 Aug 06  (Deposition) - 29 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinases, Drug, Inhibitor, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Jauch, M. K. Cho, C. Netter, K. Schreiter, B. Aicher, M. Zweckstetter, M. C. Wahl
Mitogen-Activated Protein Kinases Interacting Kinases Are Autoinhibited By A Reprogrammed Activation Segment.
Embo J. V. 25 4020 2006
PubMed-ID: 16917500  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601285

(-) Compounds

Molecule 1 - MAP KINASE-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentMNK2
    GeneMKNK2, MNK2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAP KINASE SIGNAL-INTEGRATING KINASE 2, MNK2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1STU1Ligand/IonSTAUROSPORINE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:299 , CYS A:311 , CYS A:314BINDING SITE FOR RESIDUE ZN A 41
2AC2SOFTWARELEU A:90 , GLY A:91 , GLU A:92 , ALA A:111 , LYS A:113 , GLU A:160 , LYS A:161 , MET A:162 , GLY A:165 , GLU A:209BINDING SITE FOR RESIDUE STU A 31

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:311 -A:314

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:118 -Pro A:119
2Ser A:220 -Pro A:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040805D73NMKNK2_HUMANPolymorphism56158214AD73N

  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.MKNK2_HUMAN90-113  1A:90-113
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MKNK2_HUMAN201-213  1A:201-213

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002508961ENSE00001376577chr19:2051243-2051095149MKNK2_HUMAN-00--
1.2ENST000002508962ENSE00001491579chr19:2050946-2050800147MKNK2_HUMAN1-17170--
1.3ENST000002508963ENSE00001356487chr19:2046690-204660388MKNK2_HUMAN18-47300--
1.4ENST000002508964ENSE00001340471chr19:2046467-2046366102MKNK2_HUMAN47-81351A:70-81 (gaps)13
1.5ENST000002508965ENSE00000655558chr19:2046282-204618598MKNK2_HUMAN81-113331A:81-11333
1.6ENST000002508966ENSE00000892339chr19:2043581-204350280MKNK2_HUMAN114-140271A:114-14027
1.7ENST000002508967ENSE00000655556chr19:2043196-204312374MKNK2_HUMAN140-165261A:140-16526
1.8ENST000002508968ENSE00000655555chr19:2042869-2042765105MKNK2_HUMAN165-200361A:165-20036
1.9ENST000002508969ENSE00000951200chr19:2042661-204260656MKNK2_HUMAN200-218191A:200-21819
1.10ENST0000025089610ENSE00000892334chr19:2042521-204242696MKNK2_HUMAN219-250321A:219-22810
1.11ENST0000025089611ENSE00000892331chr19:2042033-2041839195MKNK2_HUMAN251-315651A:252-315 (gaps)64
1.12ENST0000025089612ENSE00001735019chr19:2041203-2041039165MKNK2_HUMAN316-370551A:316-37055
1.13ENST0000025089613ENSE00000892327chr19:2040176-204013344MKNK2_HUMAN371-385151A:371-3711
1.14aENST0000025089614aENSE00001151082chr19:2039855-20374812375MKNK2_HUMAN385-465810--

(-) 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:271
 aligned with MKNK2_HUMAN | Q9HBH9 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:303
                                    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       368   
          MKNK2_HUMAN    69 GRATDSFSGRFEDVYQLQEDVLGEGAHARVQTCINLITSQEYAVKIIEKQPGHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMRGGSILSHIHKRRHFNELEASVVVQDVASALDFLHNKGIAHRDLKPENILCEHPNQVSPVKICDFDLGSGIKLNGDCSPISTPELLTPCGSAEYMAPEVVEAFSEEASIYDKRCDLWSLGVILYILLSGYPPFVGRCGSDCGWDRGEACPACQNMLFESIQEGKYEFPDKDWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQGC 371
               SCOP domains d 2hw7a_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains - -----------2hw7A01 A:82-161 Phosphorylase Kinase; domain 1                                 2hw7A02 A:162-371 Transferase(Phosphotransferase) domain 1                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-.......hhhhheee..........eeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee....-----------------------.hhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhh........---..-----...hhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4     --------------------------------Exon 1.6  PDB: A:114-140   ------------------------Exon 1.8  PDB: A:165-200            ------------------Exon 1.10  PDB: A:219-228       Exon 1.11  PDB: A:252-315 (gaps) UniProt: 251-315 [INCOMPLETE]   Exon 1.12  PDB: A:316-370 UniProt: 316-370             1 Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.5  PDB: A:81-113          --------------------------Exon 1.7  PDB: A:140-165  ----------------------------------Exon 1.9           --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2hw7 A  70 G-STDSFSGRFEDVYQLQEDVLGEGAHARVQTCINLITSQEYAVKIIEKQPGHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMRGGSILSHIHKRRHFNELEASVVVQDVASALDFLHNKGIAHRDLKPENILCEHPNQVSPVKICDFG-----------------------GSAEYMAPEVVEAFSEEASIYDKRCDLWSLGVILYILLSGYPPFVGRC---CG-----ACPACQNMLFESIQEGKYEFPDKDWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQGC 371
                            | |     78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         -         -   |   258       268       278       288       298|   ||   - |     318       328       338       348       358       368   
                            | |                                                                                                                                                          228                     252                                            299 303|   310                                                             
                           70 |                                                                                                                                                                                                                                      304                                                                   
                             71                                                                                                                                                                                                                                                                                                            

   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 2HW7)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MKNK2_HUMAN | Q9HBH9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0009931    calcium-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    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: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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071243    cellular response to arsenic-containing substance    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 arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    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 withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    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: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: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:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        MKNK2_HUMAN | Q9HBH92ac3 2ac5

(-) Related Entries Specified in the PDB File

2ac3 2AC3 IS THE CRYSTAL STRUCTURE OF HUMAN MNK2 KINASE DOMAIN AT 2.10 ANGSTROM RESOLUTION
2ac5 2AC5 IS THE CRYSTAL STRUCTURE OF HUMAN MNK2 KINASE DOMAIN D228G MUTANT AT 3.20 ANGSTROM RESOLUTION
2hw6 2HW6 IS THE CRYSTAL STRUCTURE OF HUMAN MNK1 KINASE CATALYTIC DOMAIN AT 2.50 ANGSTROM RESOLUTION