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(-) Description

Title :  CDK8-CYCC IN COMPLEX WITH [6-HYDROXY-3-(3-METHYL-BENZYL)-1H-INDAZOL-5-YL]-((S)-3-HYDROXY-PYRROLIDIN-1-YL)-METHANONE
 
Authors :  D. Musil, J. Blagg, K. Schiemann
Date :  18 Jan 16  (Deposition) - 27 Apr 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cdk8 Kinase / Cyclin C, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Schiemann
Cdk8-Cycc In Complex With [6-Hydroxy-3-(3-Methyl-Benzyl)-1H-Indazol-5-Yl]-((S) -3-Hydroxy-Pyrrolidin-1-Yl)-Methanone
To Be Published
PubMed: search

(-) 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
    Fragment: KINASE DOMAIN, RESIDUES 1-362
    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
    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, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
162M1Ligand/Ion[6-HYDROXY-3-(3-METHYLBENZYL)-1H-INDAZOL-5-YL][(3S)-3-HYDROXYPYRROLIDIN-1-YL]METHANONE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FMT6Ligand/IonFORMIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:27 , GLY A:28 , TYR A:32 , VAL A:35 , ALA A:50 , LYS A:52 , PHE A:97 , ASP A:98 , TYR A:99 , ALA A:100 , ALA A:155 , ASN A:156 , LEU A:158 , ASP A:173 , ARG A:356 , FMT A:402binding site for residue 62M A 401
2AC2SOFTWAREGLU A:66 , ASP A:173 , PHE A:176 , 62M A:401binding site for residue FMT A 402
3AC3SOFTWAREARG A:150 , HOH A:505 , HOH A:525 , HOH A:532binding site for residue FMT A 403
4AC4SOFTWAREARG A:71 , GLU A:72 , HOH A:527 , GLN B:7binding site for residue FMT A 404
5AC5SOFTWAREGLU A:165 , ARG A:166 , ARG A:168binding site for residue FMT A 405
6AC6SOFTWAREVAL A:302 , LYS A:303binding site for residue FMT A 406
7AC7SOFTWAREGLN B:13binding site for residue EDO B 301
8AC8SOFTWAREGLN B:41 , LYS B:70 , TYR B:73binding site for residue EDO B 302
9AC9SOFTWAREPRO B:194 , PHE B:195 , HOH B:418binding site for residue FMT B 303

(-) SS Bonds  (0, 0)

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

(-) 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 5HNB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HNB)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhee....eeee...eeeeeeee........eeeeee.....hhhhhhhhhhhhhh.......eeeeeee....eeeeeee...eehhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.........eee......hhhhh........hhhhhh.....hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hnb A  -2 DDKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKALPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQESNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFL 359
                                     7        17        27        37        47        57        67        77        87        97       107       123       133       143       153       163       173       183 ||    203       213       223       233     ||247       257       267       277       287       297       307       317       327       337       347       357  
                                                                                                                                                116|                                                           185|                                        239|                                                                                                                   
                                                                                                                                                 123                                                            196                                         244                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hnb 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 5HNB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  5hnb
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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 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hvy 5i5z 5icp 5idn 5idp
        CDK8_HUMAN | P49336: 3rgf 4crl 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hvy 5i5z 5icp 5idn 5idp

(-) Related Entries Specified in the PDB File

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