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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CDK8/CYCC IN COMPLEX WITH COMPOUND 7 (1-[3-TERT-BUTYL-1-(4-METHYLPHENYL)-1H-PYRAZOL-5-YL]UREA)
 
Authors :  E. V. Schneider, J. Boettcher, R. Huber, K. Maskos
Date :  15 May 12  (Deposition) - 01 May 13  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Kinase Complex, Proteros, Transferase-Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Schneider, J. Bottcher, R. Huber, K. Maskos, L. Neumann
Structure-Kinetic Relationship Study Of Cdk8/Cycc Specific Compounds.
Proc. Natl. Acad. Sci. Usa V. 110 8081 2013
PubMed-ID: 23630251  |  Reference-DOI: 10.1073/PNAS.1305378110

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 8
    Chains: A
    EC Number: 2.7.11.22, 2.7.11.23
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 1-403
    Gene: CDK8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 8, MEDIATOR COMPLEX SUBUNIT CDK8, MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8, PROTEIN KINASE K35
 
Molecule 2 - CYCLIN-C
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: CCNC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRB11 HOMOLOG, HSRB11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
10SQ1Ligand/Ion1-[3-TERT-BUTYL-1-(4-METHYLPHENYL)-1H-PYRAZOL-5-YL]UREA
2EDO4Ligand/Ion1,2-ETHANEDIOL
3FMT7Ligand/IonFORMIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:32 , SER A:62 , GLU A:66 , LEU A:73 , ILE A:79 , HIS A:149 , ALA A:172 , ASP A:173BINDING SITE FOR RESIDUE 0SQ A 501
02AC2SOFTWAREASP A:98 , ALA A:100 , LEU A:158 , HOH A:649BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREARG A:150 , TYR A:211BINDING SITE FOR RESIDUE FMT A 503
04AC4SOFTWAREARG A:65 , ARG A:150BINDING SITE FOR RESIDUE FMT A 504
05AC5SOFTWAREARG A:71 , HOH A:648BINDING SITE FOR RESIDUE FMT A 505
06AC6SOFTWAREILE A:79 , SER A:80 , ASP A:98 , GLU A:165BINDING SITE FOR RESIDUE FMT A 506
07AC7SOFTWAREGLN B:41 , LYS B:70 , FMT B:304BINDING SITE FOR RESIDUE EDO B 301
08AC8SOFTWARETYR B:153 , HIS B:154 , TYR B:156 , ARG B:157BINDING SITE FOR RESIDUE EDO B 302
09AC9SOFTWAREALA B:0 , GLU B:98 , ILE B:151BINDING SITE FOR RESIDUE EDO B 303
10BC1SOFTWAREGLN B:41 , THR B:45 , THR B:66 , PHE B:69 , LYS B:70 , EDO B:301BINDING SITE FOR RESIDUE FMT B 304
11BC2SOFTWAREGLN B:49 , GLN B:59 , ALA B:63 , TYR B:156BINDING SITE FOR RESIDUE FMT B 305
12BC3SOFTWAREPHE B:5 , PRO B:194 , PHE B:195BINDING SITE FOR RESIDUE FMT B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F6S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:338 -Pro A:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F6S)

(-) Exons   (0, 0)

(no "Exon" information available for 4F6S)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhee....eee....eeeeeeee........eeeeee.....hhhhhhhhhhhh.........eeeeeee....eeeeeee...eehhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhh.eee.........eee............hhhhhh.....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f6s A   0 KMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFAVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFL 359
                                     9        19        29        39        49        59        69        79        89        99       109    || 127       137       147       157       167       177|      204       214       224       234  ||   251       261       271       281       291       301       311       321       331       341       351        
                                                                                                                                            114|                                                   177|                                       237|                                                                                                                  
                                                                                                                                             123                                                    195                                        245                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f6s B  -1 KAMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPP 264
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
   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 4F6S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F6S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F6S)

(-) Gene Ontology  (27, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:338 - Pro A:339   [ RasMol ]  
 

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  4f6s
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  CDK8_HUMAN | P49336
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  2.7.11.22
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  2.7.11.23
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 Related Entries

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

UniProtKB/Swiss-Prot
        CCNC_HUMAN | P24863: 3rgf 4crl 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp
        CDK8_HUMAN | P49336: 3rgf 4crl 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp

(-) Related Entries Specified in the PDB File

4f6u 4f6w 4f70 4f7j 4f7l 4f7n