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(-) Description

Title :  RSK2 C-TERMINAL KINASE DOMAIN WITH INHIBITOR (E)-METHYL 3-(4-AMINO-7-(3-HYDROXYPROPYL)-5-P-TOLYL-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-2-CYANOACRYLATE
 
Authors :  I. M. Serafimova, M. A. Pufall, S. Krishnan, K. Duda, M. S. Cohen, R. L. Ma J. M. Mcfarland, R. M. Miller, M. Frodin, J. Taunton
Date :  12 Jan 12  (Deposition) - 25 Apr 12  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Kinase, Inhibitor, Reversible, Thiol, Phosphorylation, Migration, , Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. M. Serafimova, M. A. Pufall, S. Krishnan, K. Duda, M. S. Cohen, R. L. Maglathlin, J. M. Mcfarland, R. M. Miller, M. Frodin, J. Taunton
Reversible Targeting Of Noncatalytic Cysteines With Chemically Tuned Electrophiles.
Nat. Chem. Biol. V. 8 471 2012
PubMed-ID: 22466421  |  Reference-DOI: 10.1038/NCHEMBIO.925

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 KINASE ALPHA-3
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET46
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL KINASE DOMAIN, UNP RESIDUES 399-740
    GeneISPK1, MAPKAPK1B, RPS6KA3, RSK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymS6K-ALPHA-3, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 3, P90-RSK 3, P90RSK3, INSULIN-STIMULATED PROTEIN KINASE 1, ISPK-1, MAP KINASE- ACTIVATED PROTEIN KINASE 1B, MAPK-ACTIVATED PROTEIN KINASE 1B, MAPKAP KINASE 1B, MAPKAPK-1B, RIBOSOMAL S6 KINASE 2, RSK-2, PP90RSK2

 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
10JG1Ligand/IonMETHYL (2S)-3-{4-AMINO-7-[(1E)-3-HYDROXYPROP-1-EN-1-YL]-5-(4-METHYLPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL}-2-CYANOPROPANOATE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10JG1Ligand/IonMETHYL (2S)-3-{4-AMINO-7-[(1E)-3-HYDROXYPROP-1-EN-1-YL]-5-(4-METHYLPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL}-2-CYANOPROPANOATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
10JG2Ligand/IonMETHYL (2S)-3-{4-AMINO-7-[(1E)-3-HYDROXYPROP-1-EN-1-YL]-5-(4-METHYLPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL}-2-CYANOPROPANOATE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:428 , SER A:434 , CYS A:436 , ALA A:449 , LYS A:451 , VAL A:491 , THR A:493 , GLU A:494 , MET A:496 , CYS A:560 , ASP A:561BINDING SITE FOR RESIDUE 0JG A 900
2AC2SOFTWAREGLY A:471 , HIS A:473 , ILE A:476 , THR A:478 , HOH A:1007BINDING SITE FOR RESIDUE NA A 901

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:579 -A:579

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D9T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035627I416VKS6A3_HUMANUnclassified148050184AI416V
2UniProtVAR_006196G431DKS6A3_HUMANDisease (CLS)  ---AG431D
3UniProtVAR_040629Y483CKS6A3_HUMANUnclassified  ---AY483C
4UniProtVAR_040630L608FKS6A3_HUMANUnclassified  ---AL608F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035627I416VKS6A3_HUMANUnclassified148050184AI416V
2UniProtVAR_006196G431DKS6A3_HUMANDisease (CLS)  ---AG431D
3UniProtVAR_040629Y483CKS6A3_HUMANUnclassified  ---AY483C
4UniProtVAR_040630L608FKS6A3_HUMANUnclassified  ---AL608F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035627I416VKS6A3_HUMANUnclassified148050184AI416V
2UniProtVAR_006196G431DKS6A3_HUMANDisease (CLS)  ---AG431D
3UniProtVAR_040629Y483CKS6A3_HUMANUnclassified  ---AY483C
4UniProtVAR_040630L608FKS6A3_HUMANUnclassified  ---AL608F

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A3_HUMAN74-100
428-451
  1-
A:428-451
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A3_HUMAN189-201
535-547
  1-
A:535-547
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A3_HUMAN74-100
428-451
  1-
A:428-451
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A3_HUMAN189-201
535-547
  1-
A:535-547
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A3_HUMAN74-100
428-451
  2-
A:428-451
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A3_HUMAN189-201
535-547
  2-
A:535-547

(-) Exons   (0, 0)

(no "Exon" information available for 4D9T)

(-) 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:299
 aligned with KS6A3_HUMAN | P51812 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:299
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704         
          KS6A3_HUMAN   415 SIQFTDGYEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWIVHWDQLPQYQLNRQDAPHLVKGAMAATYSALNRN 713
               SCOP domains d4d9ta_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee...eeeeeeee....eeeeeeeee.....hhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....hhh.eee......ee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh............hhhhhhhhhhhh........hhhhhh.hhhhhhhhhh.........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -V--------------D---------------------------------------------------C----------------------------------------------------------------------------------------------------------------------------F--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9t A 415 SIQFTDGYEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLERQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWIVHWDQLPQYQLNRQDAPHLVKGAMAATYSALNRN 713
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704         

   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 4D9T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D9T)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A   (KS6A3_HUMAN | P51812)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    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: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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    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:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043620    regulation of DNA-templated transcription in response to stress    Modulation of the frequency, rate or extent of transcription from a DNA template as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0043555    regulation of translation in response to stress    Modulation of the frequency, rate or extent of translation as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    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:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0002224    toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
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
        KS6A3_HUMAN | P518124d9u 4jg6 4jg7 4jg8 4nus 4nw5 4nw6 5d9k 5d9l

(-) Related Entries Specified in the PDB File

4d9u