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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CDC-LIKE KINASE 3 ISOFORM IN COMPLEX WITH LEUCETTINE L41
 
Authors :  P. Filippakopoulos, O. Fedorov, O. King, M. Debdab, F. Carreaux, S. Ren A. Bullock, J. R. C. Muniz, F. Von Delft, C. H. Arrowsmith, A. M. Edward J. Weigelt, C. Bountra, L. Meijer, J. P. Bazureau, S. Knapp, Structura Genomics Consortium (Sgc)
Date :  28 Mar 11  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Kinase, Tyrosine-Protein Kinase, Serine/Threonine- Protein Kinase, Nucleotide-Binding, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, O. Fedorov, O. King, A. Bullock, J. R. C. Muniz, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Cdc-Like Kinase 3 Isoform With A Benzo-Dioxol Ligand
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE CLK3
    ChainsA, B
    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
    FragmentRESIDUES 275-632
    GeneCLK3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCDC-LIKE KINASE 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13RA2Ligand/Ion5-(1,3-BENZODIOXOL-5-YLMETHYL)-2-(PHENYLAMINO)-4H-IMIDAZOL-4-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13RA1Ligand/Ion5-(1,3-BENZODIOXOL-5-YLMETHYL)-2-(PHENYLAMINO)-4H-IMIDAZOL-4-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13RA1Ligand/Ion5-(1,3-BENZODIOXOL-5-YLMETHYL)-2-(PHENYLAMINO)-4H-IMIDAZOL-4-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:167 , VAL A:170 , ALA A:184 , LYS A:186 , GLU A:201 , PHE A:236 , GLU A:237 , LEU A:239 , GLY A:240 , GLU A:287 , LEU A:290 , ASP A:320 , HOH A:512 , HOH A:556BINDING SITE FOR RESIDUE 3RA A 1
2AC2SOFTWAREHOH B:81 , GLU B:164 , PHE B:167 , VAL B:170 , ALA B:184 , LYS B:186 , GLU B:201 , GLU B:237 , LEU B:239 , GLY B:240 , GLU B:287 , LEU B:290 , ASP B:320 , HOH B:489 , HOH B:497 , HOH B:553BINDING SITE FOR RESIDUE 3RA B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040413R486CCLK3_HUMANPolymorphism  ---A/BR338C
2UniProtVAR_045579Q607RCLK3_HUMANPolymorphism  ---A/BQ459R
3UniProtVAR_045580R628WCLK3_HUMANPolymorphism  ---A/BR480W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040413R486CCLK3_HUMANPolymorphism  ---AR338C
2UniProtVAR_045579Q607RCLK3_HUMANPolymorphism  ---AQ459R
3UniProtVAR_045580R628WCLK3_HUMANPolymorphism  ---AR480W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040413R486CCLK3_HUMANPolymorphism  ---BR338C
2UniProtVAR_045579Q607RCLK3_HUMANPolymorphism  ---BQ459R
3UniProtVAR_045580R628WCLK3_HUMANPolymorphism  ---BR480W

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CLK3_HUMAN310-334
 
  2A:162-186
B:162-186
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CLK3_HUMAN427-439
 
  2A:279-291
B:279-291
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CLK3_HUMAN310-334
 
  1A:162-186
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CLK3_HUMAN427-439
 
  1A:279-291
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CLK3_HUMAN310-334
 
  1-
B:162-186
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CLK3_HUMAN427-439
 
  1-
B:279-291

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003950662aENSE00002172364chr15:74907335-74908239905CLK3_HUMAN-00--
1.3ENST000003950663ENSE00002172098chr15:74911538-74911689152CLK3_HUMAN1-51510--
1.4ENST000003950664ENSE00001257949chr15:74912350-74912566217CLK3_HUMAN51-123730--
1.5bENST000003950665bENSE00001257892chr15:74914461-7491455797CLK3_HUMAN124-156330--
1.6ENST000003950666ENSE00001758841chr15:74914835-7491490167CLK3_HUMAN156-178230--
1.7aENST000003950667aENSE00001795938chr15:74917243-74917359117CLK3_HUMAN178-217400--
1.8ENST000003950668ENSE00001702735chr15:74918143-74918309167CLK3_HUMAN217-273570--
1.9ENST000003950669ENSE00001775239chr15:74919693-7491978795CLK3_HUMAN273-304322A:134-156
B:136-156
23
21
1.10ENST0000039506610ENSE00001725915chr15:74919880-74920009130CLK3_HUMAN305-348442A:157-200
B:157-200
44
44
1.11ENST0000039506611ENSE00001710495chr15:74920311-7492039383CLK3_HUMAN348-375282A:200-227
B:200-227
28
28
1.12ENST0000039506612ENSE00001643549chr15:74920945-7492102480CLK3_HUMAN376-402272A:228-254
B:228-254
27
27
1.13ENST0000039506613ENSE00001592747chr15:74921283-7492137391CLK3_HUMAN402-432312A:254-284
B:254-284
31
31
1.14bENST0000039506614bENSE00002179194chr15:74922048-74922467420CLK3_HUMAN433-490582A:285-342
B:285-342
58
58

(-) 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:351
 aligned with CLK3_HUMAN | P49761 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:351
                                   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       551       561       571       581       591       601       611       621       631 
           CLK3_HUMAN   282 RSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT 632
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee...eeeeeeeee...eeeeeeee......eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee....eeeeee....eeeeee....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhh.ee..ee.....hhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------R--------------------W---- SAPs(SNPs)
                    PROSITE ----------------------------PROTEIN_KINASE_ATP       --------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.9  PDB: A:134-15Exon 1.10  PDB: A:157-200 UniProt: 305-348  ---------------------------Exon 1.12  PDB: A:228-254  ------------------------------Exon 1.14b  PDB: A:285-342 UniProt: 433-490               ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------Exon 1.11  PDB: A:200-227   --------------------------Exon 1.13  PDB: A:254-284      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3raw A 134 RSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT 484
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483 

Chain B from PDB  Type:PROTEIN  Length:349
 aligned with CLK3_HUMAN | P49761 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:349
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623         
           CLK3_HUMAN   284 VEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT 632
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------Pkinase-3rawB01 B:156-472                                                                                                                                                                                                                                                                                                    ------------ Pfam domains (1)
           Pfam domains (2) --------------------Pkinase-3rawB02 B:156-472                                                                                                                                                                                                                                                                                                    ------------ Pfam domains (2)
         Sec.struct. author .ee.....ee.....ee...eeeeeeeee...eeeeeeee.hhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee....eeeeee....eeeeee....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhh.ee..ee.....hhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------R--------------------W---- SAPs(SNPs)
                    PROSITE --------------------------PROTEIN_KINASE_ATP       --------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.9 [INCOMPLETE]Exon 1.10  PDB: B:157-200 UniProt: 305-348  ---------------------------Exon 1.12  PDB: B:228-254  ------------------------------Exon 1.14b  PDB: B:285-342 UniProt: 433-490               ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.11  PDB: B:200-227   --------------------------Exon 1.13  PDB: B:254-284      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3raw B 136 VEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT 484
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475         

   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 3RAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CLK3_HUMAN | P49761)
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: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.
biological process
    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: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:0043484    regulation of RNA splicing    Any process that modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    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:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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
        CLK3_HUMAN | P497612eu9 2exe 2wu6 2wu7

(-) Related Entries Specified in the PDB File

2eu9