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(-) Description

Title :  CRYSTAL STRUCTURE OF HISTONE LYSINE METHYLTRANSFERASE SMYD2 IN COMPLEX WITH THE METHYLTRANSFERASE INHIBITOR SINEFUNGIN
 
Authors :  Y. Jiang, N. Sirinupong, J. Brunzelle, Z. Yang
Date :  28 Feb 11  (Deposition) - 06 Jul 11  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Hsp90, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Jiang, N. Sirinupong, J. Brunzelle, Z. Yang
Crystal Structures Of Histone And P53 Methyltransferase Smyd2 Reveal A Conformational Flexibility Of The Autoinhibitory C-Terminal Domain.
Plos One V. 6 21640 2011
PubMed-ID: 21738746  |  Reference-DOI: 10.1371/JOURNAL.PONE.0021640

(-) Compounds

Molecule 1 - SET AND MYND DOMAIN-CONTAINING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSUMO
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSMYD2
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SFG1Ligand/IonSINEFUNGIN
2ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , LYS A:17 , ARG A:19 , GLU A:135 , HIS A:137 , CYS A:181 , ASN A:182 , ALA A:203 , LEU A:204 , ASN A:206 , HIS A:207 , TYR A:240 , TYR A:258 , PHE A:260 , HOH A:452 , HOH A:454 , HOH A:473 , HOH A:493 , HOH A:544 , HOH A:557 , HOH A:866BINDING SITE FOR RESIDUE SFG A 434
2AC2SOFTWARECYS A:52 , CYS A:55 , CYS A:74 , CYS A:78BINDING SITE FOR RESIDUE ZN A 435
3AC3SOFTWARECYS A:65 , CYS A:68 , HIS A:86 , CYS A:90BINDING SITE FOR RESIDUE ZN A 436
4AC4SOFTWARECYS A:209 , CYS A:262 , CYS A:264 , CYS A:267BINDING SITE FOR RESIDUE ZN A 437

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:284 -Pro A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QWW)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SMYD2_MOUSE7-241  1A:7-241
2ZF_MYND_1PS01360 Zinc finger MYND-type signature.SMYD2_MOUSE50-90  1A:50-90
3ZF_MYND_2PS50865 Zinc finger MYND-type profile.SMYD2_MOUSE52-90  1A:52-90

(-) Exons   (0, 0)

(no "Exon" information available for 3QWW)

(-) 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:430
 aligned with SMYD2_MOUSE | Q8R5A0 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:430
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432
          SMYD2_MOUSE     3 AEARGGLERFCSAGKGRGLRALRPFHVGDLLFSCPAYACVLTVGERGHHCECCFARKEGLSKCGRCKQAFYCDVECQKEDWPLHKLECSSMVVLGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVREFESHLDKLDNEKKDLIQSDIAALHQFYSKYLEFPDHSSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIHPGDEVFTSYIDLLYPTEDRNDRLRDSYFFTCECRECTTKDKDKAKVEVRKLSSPPQAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES 432
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------zf-MYND-3qwwA01 A:52-90                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------SET-3qwwA02 A:18-241                                                                                                                                                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeee.....eeeee........eeeeee..eeee.hhhh..............ee.......ee.hhhhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee........eeee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----SET  PDB: A:7-241 UniProt: 7-241                                                                                                                                                                                                           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------ZF_MYND_1  PDB: A:50-90 UniProt: 50-90   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------ZF_MYND_2  PDB: A:52-90 UniProt: 52-90 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qww A   3 AEARGGLERFCSAGKGRGLRALRPFHVGDLLFSCPAYACVLTVGERGHHCECCFARKEGLSKCGRCKQAFYCDVECQKEDWPLHKLECSSMVVLGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVREFESHLDKLDNEKKDLIQSDIAALHQFYSKYLEFPDHSSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIHPGDEVFTSYIDLLYPTEDRNDRLRDSYFFTCECRECTTKDKDKAKVEVRKLSSPPQAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES 432
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432

   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 3QWW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: TRASH (61)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMYD2_MOUSE | Q8R5A0)
molecular function
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
    GO:0046975    histone methyltransferase activity (H3-K36 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group onto lysine at position 36 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0016279    protein-lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
    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:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0010452    histone H3-K36 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0018027    peptidyl-lysine dimethylation    The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    GO:0043516    regulation of DNA damage response, signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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: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

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        SMYD2_MOUSE | Q8R5A03qwv

(-) Related Entries Specified in the PDB File

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