Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE PCTAIRE1 KINASE IN COMPLEX WITH INDIRUBIN E804
 
Authors :  T. Krojer, T. D. Sharpe, A. Roos, P. Savitsky, A. Amos, V. Ayinampudi, G. O. Fedorov, T. Keates, C. Phillips, N. Burgess-Brown, Y. Zhang, A. C. W J. Muniz, M. Vollmar, C. Thangaratnarajah, P. Rellos, E. Ugochukwu, P. Filippakopoulos, W. Yue, S. Das, F. Von Delft, A. Edwards, C. H. Arr J. Weigelt, C. Bountra, S. Knapp, A. Bullock, Structural Genomics C (Sgc)
Date :  30 Apr 10  (Deposition) - 09 Jun 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Pctaire1, Kinase, Indirubin, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Krojer, T. D. Sharpe, A. Roos, P. Savitsky, A. Amos, V. Ayinampudi, G. Berridge, O. Fedorov, T. Keates, C. Phillips, N. Burgess-Brown, Y. Zhang, A. C. W. Pike, J. Muniz, M. Vollmar, C. Thangaratnarajah, P. Rellos, E. Ugochukwu, P. Filippakopoulos, W. Yue, S. Das, F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, S. Knapp, A. Bullock
Crystal Structure Of The Pctaire1 Kinase In Complex With Indirubin E804
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN KINASE 16
    ChainsA
    EC Number2.7.11.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CH
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES IN UNP 163-478
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE/THREONINE-PROTEIN KINASE PCTAIRE-1, PCTAIRE-MOTIF PROTEIN KINASE 1

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FEF1Ligand/Ion(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FEF1Ligand/Ion(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FEF2Ligand/Ion(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:25 , GLU A:173 , VAL A:179 , ALA A:192 , VAL A:224 , GLU A:241 , TYR A:242 , LEU A:243 , ASP A:244 , GLN A:249 , GLN A:290 , ASN A:291 , LEU A:293 , ASP A:304 , PHE A:305BINDING SITE FOR RESIDUE FEF A 668

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MTL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDK16_HUMAN171-194  1A:171-194
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDK16_HUMAN282-294  1A:282-294
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDK16_HUMAN171-194  1A:171-194
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDK16_HUMAN282-294  1A:282-294
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDK16_HUMAN171-194  2A:171-194
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDK16_HUMAN282-294  2A:282-294

(-) Exons   (0, 0)

(no "Exon" information available for 3MTL)

(-) 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:294
 aligned with CDK16_HUMAN | Q00536 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:312
                                   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  
          CDK16_HUMAN   162 LETYIKLDKLGEGTYATVYKGKSKLTDNLVALKEIRLEHEEGAPCTAIREVSLLKDLKHANIVTLHDIIHTEKSLTLVFEYLDKDLKQYLDDCGNIINMHNVKLFLFQLLRGLAYCHRQKVLHRDLKPQNLLINERGELKLADFGLARAKSIPTKTYSNEVVTLWYRPPDILLGSTDYSTQIDMWGVGCIFYEMATGRPLFPGSTVEEQLHFIFRILGTPTEETWPGILSNEEFKTYNYPKYRAEALLSHAPRLDSDGADLLTKLLQFEGRNRISAEDAMKHPFFLSLGERIHKLPDTTSIFALKEIQLQKE 473
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---Pkinase-3mtlA01 A:165-446                                                                                                                                                                                                                                                                 --------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...eeeeeeee.....eeeeeee..------......hhhhhh.........eeeeee....eeeeee...eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eee...hhh.eee.....eee....eee..------------hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhh........hhhhhh...hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh..........hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mtl A 162 METYIKLDKLGEGTYATVYKGKSKLTDNLVALKEIRL------PCTAIREVSLLKDLKHANIVTLHDIIHTEKSLTLVFEYLDKDLKQYLDDCGNIINMHNVKLFLFQLLRGLAYCHRQKVLHRDLKPQNLLINERGELKLADFGLARAK------------TLWYRPPDILLGSTDYSTQIDMWGVGCIFYEMATGRPLFPGSTVEEQLHFIFRILGTPTEETWPGILSNEEFKTYNYPKYRAEALLSHAPRLDSDGADLLTKLLQFEGRNRISAEDAMKHPFFLSLGERIHKLPDTTSIFALKEIQLQKE 473
                                   171       181       191      |  -   |   211       221       231       241       251       261       271       281       291       301       311         -  |    331       341       351       361       371       381       391       401       411       421       431       441       451       461       471  
                                                              198    205                                                                                                       311          324                                                                                                                                                     

   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 3MTL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (CDK16_HUMAN | Q00536)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004693    cyclin-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK).
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0030252    growth hormone secretion    The regulated release of growth hormone from secretory granules into the blood.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0061178    regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FEF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mtl)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3mtl
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CDK16_HUMAN | Q00536
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.22
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CDK16_HUMAN | Q00536
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CDK16_HUMAN | Q005365g6v

(-) Related Entries Specified in the PDB File

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