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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN CDK12-CYCLINK COMPLEX
 
Authors :  S. E. Dixon Clarke, J. M. Elkins, A. C. W. Pike, A. Mackenzie, S. Goubin, C. Strain-Damerell, P. Mahajan, C. Tallant, R. Chalk, H. Wiggers, J. K F. Fitzpatrick, N. Burgess-Brown, E. P. Carpenter, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. Bullock
Date :  14 Aug 15  (Deposition) - 15 Jun 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,D  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zhang, N. Kwiatkowski, C. M. Olson, S. E. Dixon-Clarke, B. J. Abraham, A. K. Greifenberg, S. B. Ficarro, J. M. Elkins, Y. Liang, N. M. Hannett, T. Manz, M. Hao, B. Bartkowiak, A. L. Greenleaf, J. A. Marto, M. Geyer, A. N. Bullock, R. A. Young, N. S. Gray
Covalent Targeting Of Remote Cysteine Residues To Develop Cdk12 And Cdk13 Inhibitors.
Nat. Chem. Biol. V. 12 876 2016
PubMed-ID: 27571479  |  Reference-DOI: 10.1038/NCHEMBIO.2166

(-) Compounds

Molecule 1 - CYCLIN-K
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CCNK
 
Molecule 2 - CYCLIN-DEPENDENT KINASE 12
    Chains: C, D
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDC2-RELATED KINASE, ARGININE/SERINE-RICH, CRKRS, CELL DIVISION CYCLE 2-RELATED PROTEIN KINASE 7, CDC2-RELATED PROTEIN KINASE 7, CELL DIVISION PROTEIN KINASE 12, HCDK12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  BC 
Biological Unit 2 (1x): A  D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
15I12Ligand/IonN-[4-[(3R)-3-[[5-CHLORANYL-4-(1H-INDOL-3-YL)PYRIMIDIN-2-YL]AMINO]PIPERIDIN-1-YL]CARBONYLPHENYL]-4-(DIMETHYLAMINO)BUTANAMIDE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
15I11Ligand/IonN-[4-[(3R)-3-[[5-CHLORANYL-4-(1H-INDOL-3-YL)PYRIMIDIN-2-YL]AMINO]PIPERIDIN-1-YL]CARBONYLPHENYL]-4-(DIMETHYLAMINO)BUTANAMIDE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
15I11Ligand/IonN-[4-[(3R)-3-[[5-CHLORANYL-4-(1H-INDOL-3-YL)PYRIMIDIN-2-YL]AMINO]PIPERIDIN-1-YL]CARBONYLPHENYL]-4-(DIMETHYLAMINO)BUTANAMIDE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE C:733 , GLU C:735 , VAL C:741 , LYS C:743 , ALA C:754 , LYS C:756 , PHE C:813 , GLU C:814 , MET C:816 , ASP C:817 , ASP C:819 , GLN C:1037 , CYS C:1039BINDING SITE FOR RESIDUE 5I1 C2000
2AC2SOFTWAREILE D:733 , VAL D:741 , ALA D:754 , LYS D:756 , PHE D:813 , GLU D:814 , MET D:816 , ASP D:819 , GLU D:825 , GLN D:1037 , CYS D:1039 , GLU D:1041BINDING SITE FOR RESIDUE 5I1 D2000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ACB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ACB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ACB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ACB)

(-) Exons   (0, 0)

(no "Exon" information available for 5ACB)

(-) 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:237
                                                                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5acb A   20 TKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSRRWWEQFVQDVPVDVLEDICHQILDLYSQ  260
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       233       243       253       
                                                                                                                                                                                                                                         227|                            
                                                                                                                                                                                                                                          232                            


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh....hhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5acb B   20 TKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH  267
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        


Chain C from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeee....eeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeeee.............eeeeeee...eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhh..............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5acb C  716 ESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPYtNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCH 1040
                                   725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035     
                                                                                                                                                                                                           893-TPO                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee....eeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeeee.........eeeeeee...eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhh..............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5acb D  718 DWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSRPYtNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWS 1044
                                   727       737       747       757       767       777       787       797|      811       821       831       841       851       861       871       881    || 894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044
                                                                                                         797|                                                                                 886|  |                                                                                                                                                       
                                                                                                          802                                                                                  890  |                                                                                                                                                       
                                                                                                                                                                                                  893-TPO
   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 5ACB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ACB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ACB)

(-) Gene Ontology  (42, 55)

Asymmetric Unit(hide GO term definitions)

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  5acb
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  CDK12_HUMAN | Q9NYV4
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 Related Entries

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

UniProtKB/Swiss-Prot
        CCNK_HUMAN | O75909: 2i53 4cxa 4nst 4un0 5efq
        CDK12_HUMAN | Q9NYV4: 4cxa 4nst 4un0

(-) Related Entries Specified in the PDB File

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