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(-) Description

Title :  CRYSTAL STRUCTURE OF DUAL-SPECIFICITY TYROSINE PHOSPHORYLATION REGULATED KINASE 2 (DYRK2)
 
Authors :  P. Filippakopoulos, V. Myrianthopoulos, M. Soundararajan, T. Krojer O. Fedorov, G. Berridge, J. Wang, L. Shrestha, A. C. W. Pike, E. Ugochuk Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, C. Bountra, E. Mikros Structural Genomics Consortium (Sgc)
Date :  30 Sep 09  (Deposition) - 13 Oct 09  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A
Keywords :  Dyrk2, Dual-Specificity Tyrosine-(Y)-Phosphorylation Regulated Kinase 2, Psk-H2, Kinase, Structural Genomics Consortium, Sgc, Apoptosis, Atp-Binding, Magnesium, Manganese, Nucleotide-Binding, Nucleus, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Soundararajan, A. K. Roos, P. Savitsky, P. Filippakopoulos, A. N. Kettenbach, J. V. Olsen, S. A. Gerber, J. Eswaran, S. Knapp, J. M. Elkins
Structures Of Down Syndrome Kinases, Dyrks, Reveal Mechanisms Of Kinase Activation And Substrate Recognition.
Structure V. 21 986 2013
PubMed-ID: 23665168  |  Reference-DOI: 10.1016/J.STR.2013.03.012

(-) Compounds

Molecule 1 - DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 2
    ChainsA
    EC Number2.7.12.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 146-552
    GeneDYRK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDYRK2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SEP3Mod. Amino AcidPHOSPHOSERINE
5SO42Ligand/IonSULFATE ION
6TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:378 , ASN A:381BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREARG A:421 , ASN A:425 , ALA A:426BINDING SITE FOR RESIDUE SO4 A 2
3AC3SOFTWARELYS A:284 , GLN A:285 , ARG A:288 , GLY A:290BINDING SITE FOR RESIDUE NA A 480
4AC4SOFTWAREHIS A:174BINDING SITE FOR RESIDUE CL A 481
5AC5SOFTWAREARG A:411 , LYS A:413BINDING SITE FOR RESIDUE CL A 482

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2L)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:398 -Asp A:399
2Asp A:399 -Gly A:400
3Gly A:400 -Ser A:401

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040459P198LDYRK2_HUMANUnclassified  ---AP125L
2UniProtVAR_040460H245NDYRK2_HUMANPolymorphism34166200AH172N
3UniProtVAR_040461N295SDYRK2_HUMANPolymorphism56293072AN222S
4UniProtVAR_040462R451QDYRK2_HUMANPolymorphism35688869AR378Q
5UniProtVAR_040463F455YDYRK2_HUMANPolymorphism55774594AF382Y

  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.DYRK2_HUMAN228-251  1A:155-178
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.DYRK2_HUMAN344-356  1A:271-283

(-) Exons   (0, 0)

(no "Exon" information available for 3K2L)

(-) 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:407
 aligned with DYRK2_HUMAN | Q92630 from UniProtKB/Swiss-Prot  Length:601

    Alignment length:432
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541  
          DYRK2_HUMAN   112 TTVGKTGLPVVPERQLDSIHRRQGSSTSLKSMEGMGKVKATPMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRRLPKPP 543
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhheee.------------------------....eee..hhhhhhhhhhhhh..hhhhhhhhh.................-hhhhhhh.............ee...eeeeeeeee...eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.......eee......ee.hhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhh..........eee.....eee..ee.....ee......hhhhhh....hhhhhhhhhhhh........hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------L----------------------------------------------N-------------------------------------------------S-----------------------------------------------------------------------------------------------------------------------------------------------------------Q---Y---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------PROTEIN_KINASE_ATP      --------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k2l A  60 VDLGTENLYF------------------------MGKVKATPMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMT-GPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGsFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYtyIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPsQKLLDASKRAKNFVSsKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRRLPKPP 470
                                    69         -         -    |   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|      378      |388       398       408       418       428       438       448       458       468  
                                    69                       73                                              122 |                                159-SEP                                                                                                                                              308-TPO                                                      369-SEP         385-SEP                                                                                 
                                                                                                               124                                                                                                                                                                                      309-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  (0, 0)

(no "SCOP Domain" information available for 3K2L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K2L)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DYRK2_HUMAN | Q92630)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine 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.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
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:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0042771    intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0051534    negative regulation of NFAT protein import into nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of an NFAT protein from the cytoplasm to the nucleus.
    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:0045725    positive regulation of glycogen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    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:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYRK2_HUMAN | Q926303kvw 4azf 5lxc 5lxd

(-) Related Entries Specified in the PDB File

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